--- /dev/null
+#
+# CMake project file for WHAM single chain version
+#
+
+enable_language (Fortran)
+
+#================================
+# Set source file lists
+#================================
+set(UNRES_WHAM_SRC0
+ wham_multparm.F
+ bxread.F
+ xread.F
+ cxread.F
+ enecalc1.F
+ energy_p_new.F
+ initialize_p.F
+ molread_zs.F
+ openunits.F
+ readrtns.F
+ arcos.f
+ cartder.f
+ cartprint.f
+ chainbuild.f
+ geomout.F
+ gnmr1.f
+ icant.f
+ intcor.f
+ int_from_cart.f
+ make_ensemble1.F
+ matmult.f
+ misc.f
+ mygetenv.F
+ parmread.F
+ pinorm.f
+ printmat.f
+ rescode.f
+ setup_var.f
+ slices.F
+ store_parm.F
+ timing.F
+ wham_calc1.F
+ readrtns_compar.F
+ readpdb.f
+ fitsq.f
+ contact.f
+ elecont.f
+ contfunc.f
+ cont_frag.f
+ conf_compar.F
+ match_contact.f
+ angnorm.f
+ odlodc.f
+ promienie.f
+ qwolynes.f
+ read_ref_str.F
+ rmscalc.f
+ secondary.f
+ proc_cont.f
+ define_pairs.f
+ mysort.f
+)
+
+set(UNRES_WHAM_PP_SRC
+ bxread.F
+ chainbuild.F
+ conf_compar.F
+ cxread.F
+ enecalc1.F
+ energy_p_new.F
+ geomout.F
+ initialize_p.F
+ make_ensemble1.F
+ molread_zs.F
+ mygetenv.F
+ openunits.F
+ parmread.F
+ read_ref_str.F
+ readrtns_compar.F
+ readrtns.F
+ slices.F
+ store_parm.F
+ timing.F
+ wham_calc1.F
+ wham_multparm.F
+ xread.F
+ proc_proc.c
+)
+
+
+#================================================
+# Set comipiler flags for different sourcefiles
+#================================================
+if (Fortran_COMPILER_NAME STREQUAL "ifort")
+ set(FFLAGS0 "-mcmodel=medium -g -CB -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
+ set(FFLAGS0 "-std=legacy -g -I. -I${CMAKE_CURRENT_SOURCE_DIR}/include_unres" )
+endif (Fortran_COMPILER_NAME STREQUAL "ifort")
+
+
+#=========================================
+# Add MPI compiler flags
+#=========================================
+if(UNRES_WITH_MPI)
+ set(FFLAGS0 "${FFLAGS0} -I${MPIF_INCLUDE_DIRECTORIES}")
+endif(UNRES_WITH_MPI)
+
+set_property(SOURCE ${UNRES_WHAM_SRC0} PROPERTY COMPILE_FLAGS ${FFLAGS0} )
+
+#=========================================
+# WHAM preprocesor flags
+#=========================================
+
+set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DCRYST_BOND -DCRYST_THETA -DCRYST_SC" )
+
+#=========================================
+# System specific flags
+#=========================================
+if(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+ set(CPPFLAGS "${CPPFLAGS} -DLINUX")
+endif(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+
+#=========================================
+# Compiler specific flags
+#=========================================
+
+if (Fortran_COMPILER_NAME STREQUAL "ifort")
+ # Add ifort preprocessor flags
+ set(CPPFLAGS "${CPPFLAGS} -DPGI")
+elseif (Fortran_COMPILER_NAME STREQUAL "f95")
+ # Add new gfortran flags
+ set(CPPFLAGS "${CPPFLAGS} -DG77")
+elseif (Fortran_COMPILER_NAME STREQUAL "gfortran")
+ # Add old gfortran flags
+ set(CPPFLAGS "${CPPFLAGS} -DG77")
+endif (Fortran_COMPILER_NAME STREQUAL "ifort")
+
+#=========================================
+# Add MPI preprocessor flags
+#=========================================
+set(CPPFLAGS "${CPPFLAGS} -DMPI")
+
+#=========================================
+# Add 64-bit specific preprocessor flags
+#=========================================
+if (architektura STREQUAL "64")
+ set(CPPFLAGS "${CPPFLAGS} -DAMD64")
+endif (architektura STREQUAL "64")
+
+#=========================================
+# Apply preprocesor flags to *.F files
+#=========================================
+set_property(SOURCE ${UNRES_WHAM_PP_SRC} PROPERTY COMPILE_DEFINITIONS ${CPPFLAGS} )
+
+
+#========================================
+# Setting binary name
+#========================================
+set(UNRES_WHAM_BIN "wham_${Fortran_COMPILER_NAME}.exe")
+
+#=========================================
+# cinfo.f workaround for CMake
+#=========================================
+# get the current date
+TODAY(DATE)
+# generate cinfo.f
+
+set(CINFO "${CMAKE_CURRENT_BINARY_DIR}/cinfo.f")
+FILE(WRITE ${CINFO}
+"C CMake generated file
+ subroutine cinfo
+ include 'COMMON.IOUNITS'
+ write(iout,*)'++++ Compile info ++++'
+ write(iout,*)'Version ${UNRES_MAJOR}.${UNRES_MINOR} build ${UNRES_PATCH}'
+")
+
+CINFO_FORMAT(${CINFO} "Compiled" "${DATE}" )
+CINFO_FORMAT(${CINFO} "Compiled by" "$ENV{USER}@$ENV{HOST}" )
+CINFO_FORMAT(${CINFO} "OS name:" "${CMAKE_SYSTEM_NAME}" )
+CINFO_FORMAT(${CINFO} "OS release:" "${CMAKE_SYSTEM}" )
+CINFO_FORMAT(${CINFO} "Fortran Compiler:" "${CMAKE_Fortran_COMPILER}" )
+CINFO_FORMAT(${CINFO} "MD Force field:" "${UNRES_MD_FF}" )
+CINFO_FORMAT(${CINFO} "CPPFLAGS =" "${CPPFLAGS}")
+
+FILE(APPEND ${CINFO}
+" write(iout,*)'++++ End of compile info ++++'
+ return
+ end ")
+
+# set include path
+set_property(SOURCE ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f PROPERTY COMPILE_FLAGS "${FFLAGS0} -I${CMAKE_CURRENT_SOURCE_DIR}" )
+
+#=========================================
+# Set full unres CSA sources
+#=========================================
+set(UNRES_WHAM_SRCS ${UNRES_WHAM_SRC0} ${CMAKE_CURRENT_BINARY_DIR}/cinfo.f proc_proc.c)
+
+#=========================================
+# Build the binary
+#=========================================
+add_executable(UNRES_WHAM_BIN ${UNRES_WHAM_SRCS} )
+set_target_properties(UNRES_WHAM_BIN PROPERTIES OUTPUT_NAME ${UNRES_WHAM_BIN})
+
+#set_property(TARGET ${UNRES_BIN} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/unres/MD )
+#add_dependencies (${UNRES_BIN} ${UNRES_XDRFLIB})
+
+#=========================================
+# Link libraries
+#=========================================
+# link MPI library (libmpich.a)
+target_link_libraries( UNRES_WHAM_BIN ${MPIF_LIBRARIES} )
+# link libxdrf.a
+target_link_libraries( UNRES_WHAM_BIN xdrf )
+
+#=========================================
+# TESTS
+#=========================================
+
+#-- Copy all the data files from the test directory into the source directory
+#SET(UNRES_TEST_FILES
+# ala10.inp
+# )
+
+#FOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
+# SET (unres_test_dest "${CMAKE_CURRENT_BINARY_DIR}/${UNRES_TEST_FILE}")
+# MESSAGE (STATUS " Copying ${UNRES_TEST_FILE} from ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} to ${unres_test_dest}")
+# ADD_CUSTOM_COMMAND (
+# TARGET ${UNRES_BIN}
+# POST_BUILD
+# COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/examples/unres/MD/ff_gab/${UNRES_TEST_FILE} ${unres_test_dest}
+# )
+#ENDFOREACH (UNRES_TEST_FILE ${UNRES_TEST_FILES})
+
+#=========================================
+# Generate data test files
+#=========================================
+# test_single_ala.sh
+#=========================================
+
+#FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh
+#"#!/bin/sh
+#export POT=GB
+#export PREFIX=ala10
+#-----------------------------------------------------------------------------
+#UNRES_BIN=./${UNRES_BIN}
+#-----------------------------------------------------------------------------
+#DD=${CMAKE_SOURCE_DIR}/PARAM
+#export BONDPAR=$DD/bond.parm
+#export THETPAR=$DD/thetaml.5parm
+#export ROTPAR=$DD/scgauss.parm
+#export TORPAR=$DD/torsion_631Gdp.parm
+#export TORDPAR=$DD/torsion_double_631Gdp.parm
+#export ELEPAR=$DD/electr_631Gdp.parm
+#export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+#export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
+#export SCPPAR=$DD/scp.parm
+#export SCCORPAR=$DD/rotcorr_AM1.parm
+#export PATTERN=$DD/patterns.cart
+#-----------------------------------------------------------------------------
+#$UNRES_BIN
+#")
+
+#=========================================
+# ala10.inp
+#=========================================
+
+#file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/ala10.inp
+#"ala10 unblocked
+#SEED=-1111333 MD ONE_LETTER rescale_mode=2 PDBOUT
+#nstep=15000 ntwe=100 ntwx=1000 dt=0.1 lang=0 tbf t_bath=300 damax=1.0 &
+#reset_moment=1000 reset_vel=1000 MDPDB
+#WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
+#WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
+#WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
+#WVDWPP=0.11371 WHPB=1.00000 &
+#CUTOFF=7.00000 WCORR4=0.00000
+#12
+#XAAAAAAAAAAX
+# 0
+# 0
+# 90.0000 90.0000 90.0000 90.000 90.000 90.000 90.000 90.000
+# 90.0000 90.0000
+# 180.0000 180.0000 180.0000 180.000 180.000 180.000 180.000 180.000
+# 180.0000
+# 110.0000 110.0000 110.0000 100.000 110.000 100.000 110.000 110.000
+# 110.0000 110.0000
+# -120.0000 -120.0000 -120.000 -120.000 -120.000 -120.000 -120.000 -120.000
+# -120.0000 -120.0000
+#")
+
+
+# Add tests
+
+#if(NOT UNRES_WITH_MPI)
+
+# add_test(NAME UNRES_MD_Ala10 COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_single_ala.sh )
+
+#endif(NOT UNRES_WITH_MPI)
--- /dev/null
+ double precision ww_all(max_ene,max_parm),
+ & vbldp0_all(max_parm),akp_all(max_parm),
+ & vbldsc0_all(maxbondterm,ntyp,max_parm),
+ & aksc_all(maxbondterm,ntyp,max_parm),
+ & abond0_all(maxbondterm,ntyp,max_parm),
+ & a0thet_all(ntyp,max_parm),athet_all(2,ntyp,max_parm),
+ & bthet_all(2,ntyp,max_parm),polthet_all(0:3,ntyp,max_parm),
+ & gthet_all(3,ntyp,max_parm),theta0_all(ntyp,max_parm),
+ & sig0_all(ntyp,max_parm),sigc0_all(ntyp,max_parm),
+ & aa0thet_all(maxthetyp1,maxthetyp1,maxthetyp1,max_parm),
+ & aathet_all(maxtheterm,maxthetyp1,maxthetyp1,maxthetyp1,max_parm),
+ & bbthet_all(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & ccthet_all(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & ddthet_all(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & eethet_all(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & ffthet_all(maxdouble,maxdouble,maxtheterm3,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & ggthet_all(maxdouble,maxdouble,maxtheterm3,maxthetyp1,maxthetyp1,
+ & maxthetyp1,max_parm),
+ & dsc_all(ntyp1,max_parm),bsc_all(maxlob,ntyp,max_parm),
+ & censc_all(3,maxlob,ntyp,max_parm),
+ & gaussc_all(3,3,maxlob,ntyp,max_parm),dsc0_all(ntyp1,max_parm),
+ & sc_parmin_all(65,ntyp,max_parm),
+ & v0_all(maxtor,maxtor,max_parm),
+ & v1_all(maxterm,maxtor,maxtor,max_parm),
+ & v2_all(maxterm,maxtor,maxtor,max_parm),
+ & vlor1_all(maxlor,maxtor,maxtor,max_parm),
+ & vlor2_all(maxlor,maxtor,maxtor,max_parm),
+ & vlor3_all(maxlor,maxtor,maxtor,max_parm),
+ & v1c_all(2,maxtermd_1,maxtor,maxtor,maxtor,max_parm),
+ & v1s_all(2,maxtermd_1,maxtor,maxtor,maxtor,max_parm),
+ & v2c_all(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor,max_parm),
+ & v2s_all(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor,max_parm),
+ & b1_all(2,maxtor,max_parm),b2_all(2,maxtor,max_parm),
+ & cc_all(2,2,maxtor,max_parm),dd_all(2,2,maxtor,max_parm),
+ & ee_all(2,2,maxtor,max_parm),ctilde_all(2,2,maxtor,max_parm),
+ & dtilde_all(2,2,maxtor,max_parm),b1tilde_all(2,maxtor,max_parm),
+ & app_all(2,2,max_parm),bpp_all(2,2,max_parm),
+ & ael6_all(2,2,max_parm),ael3_all(2,2,max_parm),
+ & aad_all(ntyp,2,max_parm),bad_all(ntyp,2,max_parm),
+ & aa_all(ntyp,ntyp,max_parm),bb_all(ntyp,ntyp,max_parm),
+ & augm_all(ntyp,ntyp,max_parm),eps_all(ntyp,ntyp,max_parm),
+ & sigma_all(ntyp,ntyp,max_parm),r0_all(ntyp,ntyp,max_parm),
+ & chi_all(ntyp,ntyp,max_parm),chip_all(ntyp,max_parm),
+ & chipp_all(ntyp,ntyp,max_parm),sigmap1_all(ntyp,ntyp,max_parm),
+ & sigmap2_all(ntyp,ntyp,max_parm),chis_all(ntyp,ntyp,max_parm),
+ & alphasur_all(4,ntyp,ntyp,max_parm),
+ & wstate_all(4,ntyp,ntyp,max_parm),
+ & nstate_all(ntyp,ntyp,max_parm),
+ & dhead_all(2,2,ntyp,ntyp,max_parm),
+ & dtail_all(2,ntyp,ntyp,max_parm),
+ & epshead_all(ntyp,ntyp,max_parm),
+ & rborn_all(ntyp,ntyp,max_parm),
+ & wqdip_all(2,ntyp,ntyp,max_parm),wquad_all(ntyp,ntyp,max_parm),
+ & alphapol_all(ntyp,ntyp,max_parm),
+ & alphiso_all(4,ntyp,ntyp,max_parm),
+ & sigiso1_all(ntyp,ntyp,max_parm),
+ & sigiso2_all(ntyp,ntyp,max_parm),
+ & epsintab_all(ntyp,ntyp,max_parm),
+ & alp_all(ntyp,max_parm),ebr_all(max_parm),d0cm_all(max_parm),
+ & akcm_all(max_parm),akth_all(max_parm),akct_all(max_parm),
+ & v1ss_all(max_parm),v2ss_all(max_parm),v3ss_all(max_parm),
+ & v1sccor_all(maxterm_sccor,3,ntyp,ntyp,max_parm),
+ & v2sccor_all(maxterm_sccor,3,ntyp,ntyp,max_parm)
+ integer nlob_all(ntyp1,max_parm),nlor_all(maxtor,maxtor,max_parm),
+ & nterm_all(maxtor,maxtor,max_parm),
+ & ntermd1_all(maxtor,maxtor,maxtor,max_parm),
+ & ntermd2_all(maxtor,maxtor,maxtor,max_parm),
+ & nbondterm_all(ntyp,max_parm),nthetyp_all(max_parm),
+ & ithetyp_all(ntyp1,max_parm),ntheterm_all(max_parm),
+ & ntheterm2_all(max_parm),ntheterm3_all(max_parm),
+ & nsingle_all(max_parm),ndouble_all(max_parm),
+ & nntheterm_all(max_parm),nterm_sccor_all(ntyp,ntyp,max_parm)
+ common /allparm/ ww_all,vbldp0_all,akp_all,vbldsc0_all,aksc_all,
+ & abond0_all,aa0thet_all,aathet_all,bbthet_all,ccthet_all,
+ & ddthet_all,eethet_all,ffthet_all,ggthet_all,
+ & a0thet_all,athet_all,bthet_all,polthet_all,gthet_all,theta0_all,
+ & sig0_all,sigc0_all,dsc_all,bsc_all,censc_all,gaussc_all,dsc0_all,
+ & sc_parmin_all,
+ & v0_all,v1_all,v2_all,vlor1_all,vlor2_all,vlor3_all,v1c_all,
+ & v1s_all,v2c_all,v2s_all,b1_all,b2_all,cc_all,dd_all,ee_all,
+ & ctilde_all,dtilde_all,b1tilde_all,app_all,bpp_all,ael6_all,
+ & ael3_all,aad_all,bad_all,aa_all,bb_all,augm_all,
+ & eps_all,sigma_all,r0_all,chi_all,chipp_all,sigmap1_all,
+ & sigmap2_all,
+ & chis_all,alphasur_all,wstate_all,dhead_all,dtail_all,
+ & epshead_all,
+ & rborn_all,wqdip_all,wquad_all,alphapol_all,alphiso_all,
+ & sigiso1_all,
+ & sigiso2_all,epsintab_all,chip_all,alp_all,ebr_all,
+ & d0cm_all,akcm_all,akth_all,akct_all,v1ss_all,v2ss_all,v3ss_all,
+ & v1sccor_all,v2sccor_all,nbondterm_all,
+ & nlob_all,nlor_all,nterm_all,ntermd1_all,ntermd2_all,
+ & nthetyp_all,ithetyp_all,ntheterm_all,ntheterm2_all,ntheterm3_all,
+ & nsingle_all,ndouble_all,nntheterm_all,nterm_sccor_all,nstate_all
--- /dev/null
+ integer nres,nres0,nsup,nstart_sup,nend_sup,nstart_seq,ishift_pdb
+ double precision c,cref,dc,xloc,xrot,dc_norm,t,r,prod,rt
+ common /chain/ c(3,maxres2+2),dc(3,maxres2),xloc(3,maxres),
+ & xrot(3,maxres),dc_norm(3,maxres2),nres,nres0
+ common /rotmat/ t(3,3,maxres),r(3,3,maxres),prod(3,3,maxres),
+ & rt(3,3,maxres)
+ common /refstruct/ cref(3,maxres2+2),nsup,nstart_sup,nend_sup,
+ & nstart_seq,ishift_pdb
--- /dev/null
+ integer ifrag,nfrag,npiece,iclass,iscore,ishifft,ncont_nat,ibase,
+ & n_shift,ipiece,istruct,ielecont,isccont,irms,len_frag,isnfrag,
+ & nc_req_setf,iloc,iloc_single,list_frag,nlist_frag,nlevel
+ double precision rmsfrag,rmscutfrag,rmscut_base_low,
+ & rmscut_base_up,
+ & rmsup_lim,rmsupup_lim,rms_nat,rmsang,ang_cut,ang_cut1,
+ & frac_min,nc_fragm,qfrag,qnat
+ logical lgrp,lgrp_out,binary
+ integer ncreq_hel,ncreq_bet,ncreq_pair,irms_pair,icont_pair,
+ & isplit_bet,nshift_hel,nshift_bet,nshift_strand,nshift_pair,
+ & irms_single,icont_single
+ double precision angcut_hel,angcut1_hel,angcut_bet,angcut1_bet,
+ & angcut_strand,angcut1_strand,frac_min_set,ncfrac_hel,ncfrac_bet,
+ & ncfrac_pair,frac_sec
+ common /compar/ rmsfrag(maxfrag,maxlevel),
+ & qfrag(maxfrag,2),rmscut_base_low,
+ & rmscut_base_up,rmsup_lim,rmsupup_lim,
+ & rmscutfrag(2,maxfrag,maxlevel),
+ & rms_nat,qnat,rmsang,ang_cut(maxfrag),
+ & ang_cut1(maxfrag),
+ & frac_min(maxfrag),nc_fragm(maxfrag,maxlevel),
+ & nc_req_setf(maxfrag,maxlevel),
+ & ncont_nat(2,maxfrag,maxlevel),nfrag(maxlevel),
+ & isnfrag(maxlevel+1),
+ & npiece(maxfrag,maxlevel),ifrag(2,maxpiece,maxfrag),
+ & ipiece(maxpiece,maxfrag,2:maxlevel),istruct(maxfrag),
+ & ielecont(maxfrag,maxlevel),
+ & isccont(maxfrag,maxlevel),irms(maxfrag,maxlevel),
+ & iloc(maxfrag),
+ & iclass(maxlevel*maxfrag,maxlevel),
+ & iscore,ishifft(maxfrag,maxlevel),
+ & len_frag(maxfrag,maxlevel),n_shift(2,maxfrag,maxlevel),
+ & nlevel,ibase,lgrp,lgrp_out,binary,
+ & nlist_frag(maxfrag),list_frag(maxres,maxfrag)
+ common /compar1/ angcut_hel,angcut1_hel,angcut_bet,angcut1_bet,
+ & angcut_strand,angcut1_strand,frac_min_set,ncfrac_hel,ncfrac_bet,
+ & ncfrac_pair,frac_sec,ncreq_hel,ncreq_bet,ncreq_pair,irms_pair,
+ & icont_pair,isplit_bet,nshift_hel,nshift_bet,nshift_strand,
+ & nshift_pair,irms_single,icont_single,iloc_single
--- /dev/null
+ integer ncont,ncont_ref,icont,icont_ref,num_cont,jcont,
+ & nsccont_frag_ref,isccont_frag_ref
+ common /contacts/ ncont,ncont_ref,icont(2,maxcont),
+ & icont_ref(2,maxcont),nsccont_frag_ref(mmaxfrag),
+ & isccont_frag_ref(2,maxcont,mmaxfrag)
--- /dev/null
+ integer iscode,indpdb,outpdb,outmol2,icomparfunc,pdbint,
+ & ensembles,constr_dist
+ logical refstr,pdbref,punch_dist,print_rms,caonly,verbose,
+ & merge_helices,bxfile,cxfile,histfile,entfile,zscfile,
+ & rmsrgymap,with_dihed_constr,check_conf,histout,energy_dec
+ common /cntrl/ iscode,indpdb,refstr,pdbref,outpdb,outmol2,
+ & punch_dist,print_rms,caonly,verbose,icomparfunc,pdbint,
+ & merge_helices,bxfile,cxfile,histfile,entfile,zscfile,rmsrgymap,
+ & ensembles,with_dihed_constr,check_conf,histout,constr_dist,
+ & energy_dec
--- /dev/null
+ integer iscode,indpdb,outpdb,outmol2,icomparfunc,pdbint,
+ & ensembles
+ logical refstr,pdbref,punch_dist,print_rms,caonly,verbose,
+ & merge_helices,bxfile,cxfile,histfile,entfile,zscfile,
+ & rmsrgymap
+ common /cntrl/ iscode,indpdb,refstr,pdbref,outpdb,outmol2,
+ & punch_dist,print_rms,caonly,verbose,icomparfunc,pdbint,
+ & merge_helices,bxfile,cxfile,histfile,entfile,zscfile,rmsrgymap,
+ & ensembles
--- /dev/null
+c! Variable Declarations
+c! Charge of i-th residue, charge of j-th residue,...
+ INTEGER Qi, Qj, Qij, ii, jj, itypi, itypj
+
+c! STUFF FROM EMOMO
+
+c! why do *I* have to declare those guys, when it is used throughout the whole code...
+ REAL*8 evdw, evdw_p, evdw_m
+ double precision xi, yi, zi, ctail(3,2), chead(3,2)
+c! FOLLOWING ARE ***NOT*** in common block!!!
+c! They are here just for their declarations
+ REAL*8 ecl,elj,equad,epol
+ INTEGER istate
+c! intermediates
+ REAL*8 c1, c2, fac, pom
+c! switch in the selector choosing which electrostatic energy/gradient function to call
+ INTEGER isel
+c! sigma factors
+ REAL*8 sig, sig0ij, sig1, sig2
+c! intermediates related to distance
+ REAL*8 rij_shift, rrij, R1, R2, RR1, RR2
+c! intermediates related to angles
+ REAL*8 sinth1sq, sinth2sq
+c! intermediates of Fgb
+ REAL*8 fgb, ee, ee1, ee2, eps0, pis
+
+c! squares of om1, om2 and om12 (those hold cosines of angles
+c! theta)
+ REAL*8 sqom1, sqom2, sqom12
+
+c! Geometry and general stuff
+c! a12sq = ai*aj from fgb which is present in Egbpol/Fgbpol,
+c! Epol/Gpol and others, ee is an intermediate.
+c! three dimensions for X, Y and Z Cartesians
+ REAL*8 a12sq
+
+c! square distance and cartesian distances of polar/charged heads of sidechains
+ REAL*8 Rhead, Rhead_distance(3), Rhead_sq
+c! square distance and cartesian distances of tail(hydrophobic centre of interaction)
+c! of a given pair of sidechains
+ REAL*8 Rtail, Rtail_distance(3)
+c! intermediates used in dXhead/dXtail
+ REAL*8 erhead(3), ertail(3), facd1, facd2, erdxi, erdxj
+
+c! unit vectors used to calculate R's
+ REAL*8 d1sq, d2sq, d1d2
+ REAL*8 d1, d2
+
+c! intermediates (hold different meanining in different places)
+ REAL*8 bat, hawk, eagle, condor, sparrow, rosella
+ REAL*8 tuna(3)
+
+c! holds 1/eps_in - 1/eps_out which appears in EGBpol Makowski et al JPCB 2011
+c! p. 6122
+ REAL*8 eps_inout_fac, eps_in
+
+c! DERIVATIVES
+c! intermediates
+ Real*8 dFdR, dFdL, dFdOM1, dFdOM2, dFdOM12
+c! Kronecker Delta used for dXhead/dXtail derivatives
+ Real*8 kro_delta
+c! Gcl
+ REAL*8 Gelconst
+ REAL*8 dGCLdR, dGCLdOM1, dGCLdOM2, dGCLdOM12
+
+c! Ggbpol
+c! energy
+ REAL*8 Egb, dGGBdFGB, dGGBdR
+ REAL*8 dFGBdR, alphapol1, alphapol2
+
+c! Gpol
+ REAL*8 fgb1, fgb2
+ REAL*8 dPOLdOM1, dPOLdOM2, dPOLdR1, dPOLdR2
+ REAL*8 dFGBdOM1, dFGBdOM2, dFGBdR1, dFGBdR2
+ REAL*8 dPOLdFGB1, dPOLdFGB2, MomoFac1, MomoFac2
+ REAL*8 erhead_tail(3,2)
+
+c! Gisocav
+ REAL*8 Fisocav, dGCVdR
+c! alpha parameters for Fisocav/Gisocav
+ REAL*8 al1, al2, al3, al4, csig
+
+c! Gcav
+c! energy
+ REAL*8 Fcav
+c! alphas from the equation
+ REAL*8 b1, b2, b3, b4
+c! intermediates
+ Real*8 chif, lambf, chilambf
+ REAL*8 top, bot, dtop, dbot, botsq
+ REAL*8 chis1, chis2, chis12
+c! final value
+ REAL*8 dCAVdOM1, dCAVdOM2, dCAVdOM12
+
+c! Gquad stuff
+c! intermediates
+ REAL*8 wqd, w1, w2, beta1
+c! final value
+ REAl*8 dQUADdR, dQUADdOM1, dQUADdOM2, dQUADdOM12
+
+c! Glj
+c! parameter, radial derivative
+ REAL*8 eps_head, dGLJdR
+
+c! Sum of states
+ REAL*8 BetaT, eheadtail, weightbol, sumweight
+c! this thing holds intermediates and final value
+c! (dimensions, gvdw(c/x)(i/j),intermediate(1) or final(2))
+ REAL*8 gheadtail(3,4,2)
+
+c! Now Commonize what we need to
+ COMMON /emp/ Qi, Qj, Qij, ii, jj, itypi, itypj, xi, yi, zi
+ & , sqom1, sqom2, sqom12, chead, ctail
+ & , al1, al2, al3, al4
+ & , b1, b2, b3, b4
+ & , Rhead, Rhead_distance, Rtail, Rtail_distance
+ & , R1, R2, RR1, RR2
+ & , d1sq, d2sq, d1, d2, d1d2
+ & , eps_inout_fac, eps_in, wqd, eps_head, a12sq
+ & , chis1, chis2, chis12, sig1, sig2, sig0ij
+ & , BetaT
+ & , dFdR, dFdL, dFdOM1, dFdOM2, dFdOM12
+ & , dCAVdOM1, dCAVdOM2, dCAVdOM12
+ & , dGCLdOM1, dGCLdOM2, dGCLdOM12
+ & , dPOLdOM1, dPOLdOM2
+ & , dQUADdR, dQUADdOM1, dQUADdOM2, dQUADdOM12
\ No newline at end of file
--- /dev/null
+ double precision eneps_temp(2,nntyp)
+ integer n_ene
+ common /weightder/ eneps_temp,n_ene
--- /dev/null
+ double precision potE(MaxStr_Proc,Max_Parm),entfac(MaxStr_Proc),
+ & q(MaxQ+2,MaxStr_Proc),enetb(max_ene,MaxStr_Proc,Max_Parm)
+ integer einicheck
+ common /energies/ potE,entfac,q,enetb,einicheck
--- /dev/null
+ integer nQ,nparmset,stot(maxslice),rescale_mode,iparmprint,myparm
+ logical hamil_rep,separate_parset
+ double precision Kh(MaxQ,MaxR,MaxT_h,max_parm),
+ & q0(MaxQ,MaxR,MaxT_h,max_parm),delta,deltrms,deltrgy,fimin,
+ & f(maxR,maxT_h,max_parm),beta_h(MaxT_h,max_parm)
+ double precision delta_T,startGridT
+ integer nR(maxT_h,max_parm),snk(MaxR,MaxT_h,max_parm,MaxSlice),
+ & nT_h(max_parm),maxit,totraj(maxR,max_parm),nRR(maxT_h,max_parm)
+ integer nGridT
+ logical replica(max_parm),umbrella(max_parm),read_iset(max_parm)
+ common /wham/ Kh,q0,f,beta_h,delta,deltrms,deltrgy,delta_T,
+ & startGridT,fimin,snk,nR,
+ & nRR,nT_h,nQ,stot,nparmset,maxit,rescale_mode,replica,umbrella,
+ & read_iset,totraj,hamil_rep,separate_parset,iparmprint,myparm,
+ & nGridT
--- /dev/null
+C-----------------------------------------------------------------------
+C I/O units used by the program
+C-----------------------------------------------------------------------
+C 9/18/99 - unit ifourier and filename fouriername included to identify
+C the file from which the coefficients of second-order Fourier expansion
+C of the local-interaction energy are read.
+C 8/9/01 - file for SCP interaction constants named scpname (unit iscpp)
+C included.
+C-----------------------------------------------------------------------
+C General I/O units & files
+ integer inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,irotam,
+ & itorp,itordp,ifourier,ielep,isidep,iscpp,isccor,icbase,
+ & istat,ientin,ientout,isidep1,ibond,ihist,izsc,idistr
+ common /iounits/ inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,
+ & irotam,itorp,itordp,ifourier,ielep,isidep,iscpp,isccor,
+ & icbase,istat,ientin,ientout,isidep1,ibond,ihist,izsc,
+ & idistr
+ character*256 outname,intname,pdbname,mol2name,statname,intinname,
+ & entname,restartname,prefix,scratchdir,sidepname,pdbfile,
+ & histname,zscname
+ common /fnames/ outname,intname,pdbname,mol2name,statname,
+ & intinname,entname,restartname,prefix,pot,scratchdir,
+ & sidepname,pdbfile,histname,zscname
+C Parameter files
+ character*256 bondname,thetname,rotname,torname,tordname,
+ & fouriername,elename,sidename,scpname,sccorname,patname
+ common /parfiles/ thetname,rotname,torname,tordname,bondname,
+ & fouriername,elename,sidename,scpname,sccorname,patname
+ character*3 pot
+C-----------------------------------------------------------------------
+C INP - main input file
+C IOUT - list file
+C IGEOM - geometry output in the form of virtual-chain internal coordinates
+C INTIN - geometry input (for multiple conformation processing) in int. coords.
+C IPDB - Cartesian-coordinate output in PDB format
+C IMOL2 - Cartesian-coordinate output in Tripos mol2 format
+C IPDBIN - PDB input file
+C ITHEP - virtual-bond torsional angle parametrs
+C IROTAM - side-chain geometry and local-interaction parameters
+C ITORP - torsional parameters
+C ITORDP - double torsional parameters
+C IFOURIER - coefficients of the expansion of local-interaction energy
+C IELEP - electrostatic-interaction parameters
+C ISIDEP - side-chain interaction parameters.
+C ISCPP - SCp interaction parameters.
+C IBOND - virtual-bond constant parameters and moments of inertia.
+C ISCCOR - parameters of the potential of SCCOR term
+C ICBASE - data base with Cartesian coords of known structures.
+C ISTAT - energies and other conf. characteristics from an MCM run.
+C IENTIN - entropy from preceding simulation(s) to be read in.
+C-----------------------------------------------------------------------
--- /dev/null
+ integer me, me1, Master, Master1, Nprocs, Nprocs1, Comm1,
+ & Indstart, Indend, scount, idispl, i2ii, WHAM_COMM
+ integer indstart_map,indend_map,idispl_map,scount_map
+ common /MPI_Data/ Nprocs, Master,Master1,Me,Comm1,Me1,Nprocs1,
+ & WHAM_COMM,
+ & Indstart(0:MaxProcs),
+ & Indend(0:MaxProcs), idispl(0:MaxProcs),
+ & scount(0:MaxProcs)
--- /dev/null
+ real*8 time_start_collect(maxR,MaxT_h,Max_Parm),
+ & time_end_collect(maxR,MaxT_h,Max_Parm)
+ common /obcinka/ time_start_collect,time_end_collect
--- /dev/null
+ integer ncont_pept_ref,icont_pept_ref,ncont_frag_ref,
+ & icont_frag_ref,isec_ref
+ common /peptcont/ ncont_pept_ref,
+ & icont_pept_ref(2,maxcont),
+ & ncont_frag_ref(mmaxfrag),
+ & icont_frag_ref(2,maxcont,mmaxfrag),
+ & isec_ref(maxres)
--- /dev/null
+ integer ntot(maxslice),isampl(max_parm),nslice
+ common /protein/ ntot,isampl,nslice
--- /dev/null
+ character*80 protfiles(maxfile_prot,2,MaxR,MaxT_h,Max_Parm),
+ & bprotfiles
+ integer nfile_bin(MaxR,MaxT_h,Max_Parm),
+ & nfile_asc(MaxR,MaxT_h,Max_Parm),
+ & nfile_cx(MaxR,MaxT_h,Max_Parm),
+ & rec_start(MaxR,MaxT_h,Max_Parm),
+ & rec_end(MaxR,MaxT_h,Max_Parm),lenrec,lenrec1,lenrec2
+ common /protfil/ protfiles,bprotfiles,
+ & nfile_bin,nfile_asc,nfile_cx,rec_start,rec_end,lenrec,lenrec1,
+ & lenrec2
--- /dev/null
+C Store the geometric variables in the following COMMON block.
+ integer ntheta,nphi,nside,nvar,ialph,ivar
+ double precision theta,phi,alph,omeg,vbld,vbld_ref,
+ & theta_ref,phi_ref,alph_ref,omeg_ref,
+ & costtab,sinttab,cost2tab,sint2tab,
+ & xxtab,yytab,zztab,tauangle,omicron
+ common /var/ theta(maxres),phi(maxres),alph(maxres),omeg(maxres),
+ & omicron(2,maxres),tauangle(3,maxres),
+ & vbld(2*maxres),
+ & costtab(maxres), sinttab(maxres), cost2tab(maxres),
+ & sint2tab(maxres),xxtab(maxres),yytab(maxres),
+ & zztab(maxres),
+ & ialph(maxres,2),ivar(4*maxres2),ntheta,nphi,nside,nvar
+C Angles from experimental structure
+ common /varref/ vbld_ref(maxres),
+ & theta_ref(maxres),phi_ref(maxres),
+ & alph_ref(maxres),omeg_ref(maxres)
--- /dev/null
+********************************************************************************
+* Settings for the program of united-residue peptide simulation in real space *
+* *
+* ------- As of 6/23/01 ----------- *
+* *
+********************************************************************************
+c implicit real*8 (a-h,o-z)
+C Max. number of processors.
+c parameter (maxprocs=128)
+C Max. number of fine-grain processors
+c parameter (max_fg_procs=maxprocs)
+C Max. number of coarse-grain processors
+c parameter (max_cg_procs=maxprocs)
+C Max. number of AA residues
+ integer maxres
+c parameter (maxres=250)
+ parameter (maxres=400)
+C Appr. max. number of interaction sites
+ integer maxres2
+ parameter (maxres2=2*maxres)
+C Max. number of variables
+ integer maxvar
+ parameter (maxvar=4*maxres)
+C Max. number of groups of interactions that a given SC is involved in
+ integer maxint_gr
+ parameter (maxint_gr=2)
+C Max. number of derivatives of virtual-bond and side-chain vectors in theta
+C or phi.
+ integer maxdim
+ parameter (maxdim=(maxres-1)*(maxres-2)/2)
+C Max. number of SC contacts
+ integer maxcont
+ parameter (maxcont=12*maxres)
+C Max. number of contacts per residue
+ integer maxconts
+ parameter (maxconts=maxres)
+C Number of AA types (at present only natural AA's will be handled
+ integer ntyp,ntyp1
+ parameter (ntyp=20,ntyp1=ntyp+1)
+ integer nntyp
+ parameter (nntyp=ntyp*(ntyp+1)/2)
+C Max. number of types of dihedral angles & multiplicity of torsional barriers
+C and the number of terms in double torsionals
+ integer maxtor,maxterm,maxlor,maxtermd_1,maxtermd_2
+ parameter (maxtor=4,maxterm=10,maxlor=3,maxtermd_1=8,maxtermd_2=8)
+c Max number of torsional terms in SCCOR
+ integer maxterm_sccor
+ parameter (maxterm_sccor=6)
+C Max. number of residue types and parameters in expressions for
+C virtual-bond angle bending potentials
+ integer maxthetyp,maxthetyp1,maxtheterm,maxtheterm2,maxtheterm3,
+ & maxsingle,maxdouble,mmaxtheterm
+ parameter (maxthetyp=3,maxthetyp1=maxthetyp+1,maxtheterm=20,
+ & maxtheterm2=6,maxtheterm3=4,maxsingle=6,maxdouble=4,
+ & mmaxtheterm=maxtheterm)
+C Max. number of lobes in SC distribution
+ integer maxlob
+ parameter (maxlob=4)
+C Max. number of S-S bridges
+ integer maxss
+ parameter (maxss=20)
+C Max. number of dihedral angle constraints
+ integer maxdih_constr
+ parameter (maxdih_constr=maxres)
+C Max. number of patterns in the pattern database
+ integer maxseq
+ parameter (maxseq=1000)
+C Max. number of residues in a peptide in the database
+ integer maxres_base
+ parameter (maxres_base=1000)
+C Max. number of threading attempts
+ integer maxthread
+ parameter (maxthread=2000)
+C Max. number of move types in MCM
+ integer maxmovetype
+ parameter (maxmovetype=4)
+C Max. number of stored confs. in MC/MCM simulation
+ integer maxsave
+ parameter (maxsave=2000)
+C Max. number of conformations in Master's cache array
+ integer max_cache
+ parameter (max_cache=1000)
+C Max. number of conformations in the pool
+ integer max_pool
+ parameter (max_pool=1000)
+C Number of threads in deformation
+ integer max_thread,max_thread2
+ parameter (max_thread=40,max_thread2=2*max_thread)
+C Number of steps in DSM
+ integer max_step
+ parameter (max_step=1)
+C Number of structures to compare at t=0
+ integer max_threadss,max_threadss2
+ parameter (max_threadss=80,max_threadss2=2*max_threadss)
+C Maxmimum number of angles per residue
+ integer mxang
+ parameter (mxang=4)
+C Maximum number of groups of angles
+ integer mxgr
+ parameter (mxgr=2*maxres)
+C Maximum number of chains
+ integer mxch
+ parameter (mxch=1)
+C Maximum number of generated conformations
+ integer mxio
+ parameter (mxio=1000)
+C Maximum number of seed
+ integer max_seed
+ parameter (max_seed=100)
+C Maximum number of structures for ZSCORE for each protein
+ integer maxzs
+ parameter (maxzs=2)
+C Maximum number of structures stored for comparison for ZSCORE for each protein
+ integer maxzs1
+ parameter (maxzs1=6)
+C Maximum number of proteins for ZSCORE
+ integer maxprotzs
+ parameter (maxprotzs=1)
+C Maximum number of conf in rmsdbank
+ integer maxrmsdb
+ parameter (maxrmsdb=110)
+C Maximum number of bankt conformations
+ integer mxiot
+ parameter (mxiot=mxio)
+c Maximum number of conformations in MCMF
+ integer maxstr_mcmf
+ parameter (maxstr_mcmf=800)
+c Maximum number of families in MCMF
+ integer maxfam_p
+ parameter (maxfam_p=20)
+c Maximum number of structures in family in MCMF
+ integer maxstr_fam
+ parameter (maxstr_fam=40)
+C Maximum number of threads in MCMF
+ integer maxthread_mcmf
+ parameter (maxthread_mcmf=10)
+C Maximum number of SC local term fitting function coefficiants
+ integer maxsccoef
+ parameter (maxsccoef=65)
+C Maximum number of terms in SC bond-stretching potential
+ integer maxbondterm
+ parameter (maxbondterm=3)
--- /dev/null
+******************************************************************
+*
+* Array dimensions for level-based conformation comparison program:
+*
+* Max. number of conformations in the data set.
+*
+ integer maxconf
+ PARAMETER (MAXCONF=maxstr_proc)
+*
+* Max. number levels of comparison
+*
+ integer maxlevel
+ PARAMETER (MAXLEVEL=3)
+*
+* Max. number of fragments at a given level of comparison
+*
+ integer maxfrag,mmaxfrag
+ PARAMETER (MAXFRAG=30,MMAXFRAG=MAXFRAG*(MAXFRAG+1)/2)
+*
+* Max. number of pieces forming a substructure to be compared
+*
+ integer maxpiece
+ PARAMETER (MAXPIECE=20)
+*
+*******************************************************************
--- /dev/null
+ integer Max_Parm
+ integer MaxQ,MaxQ1
+ integer MaxR,MaxT_h
+ integer MaxSlice
+ parameter (Max_Parm=1)
+ parameter (MaxQ=4,MaxQ1=MaxQ+2)
+ parameter(MaxR=1,MaxT_h=32)
+ parameter(MaxSlice=40)
+ integer MaxN
+ parameter (MaxN=100)
+ integer MaxPrintConf
+ parameter (MaxPrintConf=1000)
+ integer Max_GridT
+ parameter (Max_GridT=400)
--- /dev/null
+ integer Max_Parm
+ integer MaxQ,MaxQ1
+ integer MaxR,MaxT_h
+ integer MaxSlice
+ parameter (Max_Parm=6)
+ parameter (MaxQ=5,MaxQ1=MaxQ+2)
+ parameter(MaxR=1,MaxT_h=32)
+ parameter(MaxSlice=40)
+ integer MaxN
+ parameter (MaxN=100)
+ integer MaxPrintConf
+ parameter (MaxPrintConf=1000)
--- /dev/null
+ integer maxstr,max_ene,maxprot,maxclass,maxfile_prot,maxobj,
+ & maxstr_proc, maxclass1
+c Maximum number of structures in the database, energy components, proteins,
+c and structural classes
+c#ifdef JUBL
+ parameter (maxstr=200000,max_ene=21,maxprot=7,maxclass=5000)
+ parameter (maxclass1=10)
+c Maximum number of structures to be dealt with by one processor
+ parameter (maxstr_proc=20000)
+c Maximum number of temperatures
+ integer maxT
+ parameter (maxT=10)
+c Maximum number of batches
+ integer maxbatch
+ parameter (maxbatch=1)
+c Maximum number of energy/Zscore gaps for a single protein
+ integer maxgap
+ parameter (maxgap=2*maxclass1)
+c Maximum number of the components of the target function
+ parameter (maxobj=maxgap*maxprot*maxT)
+c Maximum number of files with energies/coordinates
+ parameter (maxfile_prot=100)
+c Maximum number of grid points in energy map evaluation
+ integer max_x,max_y,max_minim
+ parameter (max_x=200,max_y=200,max_minim=1000)
+c Maximum number of processors
+ integer MaxProcs
+ parameter (MaxProcs = 2048)
+c Maximum number of optimizable parameters
+ integer max_paropt
+ parameter (max_paropt=500)
+c Maximum number of fragments
+c integer maxfrag
+c parameter (maxfrag=0)
+c Maximum number of sublevels
+ integer maxlev
+ parameter (maxlev=maxclass)
+c Maximum number of grid points in temperature
+ integer MaxGridT
+ parameter (MaxGridT=2000)
--- /dev/null
+Makefile_MPICH_ifort
\ No newline at end of file
--- /dev/null
+BIN = /users/adam/ZSCOREZ/bin
+CC = cc
+FC = mpif90
+#FC = ifc
+OPT = -fast -pc 64 -tp p6 -Minline=name:scalar2,scalar,transpose2,matvec2,prodmat3
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres
+#FFLAGS = ${OPT} -c -C -g -I. -I./include_unres
+FFLAGS = ${OPT} -c -I. -I./include_unres
+LIBS = -L../../MEY_MD/src_Tc/xdrf -lxdrf
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} -Wl,-Bstatic ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -o ${BIN}/wham_multparm-T-sccor
+
+clean:
+ /bin/rm *.o
--- /dev/null
+BIN = ../bin
+CC = cc
+FC = mpxlf90 -qfixed -w
+OPT = -q64
+FFLAGS = -c ${OPT} -O3 -I./include_unres
+LIBS = xdrf/libxdrf.o xdrf/ftocstr.o
+CPPFLAGS = -WF,-DMPI -WF,-DAIX -WF,-DUNRES -WF,-DSPLITELE -WF,-DPROCOR -WF,-DISNAN
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ rescode.o \
+ setup_var.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -o ${BIN}/wham_multparm1-T-procor
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+BIN = /users/adam/unres/bin/wham
+FC= ifort
+#OPT = -mcmodel=medium -O3 -ip -w
+OPT = -mcmodel=medium -g -CA -CB
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ gnmr1.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+GABs: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCALREP
+GABs: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-KN-DEBUG-scalrep.exe
+
+GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 \
+ -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DNEWCORR
+GAB: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-KN-NEWC.exe
+
+E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64 -DNEWCORR
+E0LL2Y: ${objects} ${objects_compar} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_ifort_MPICH_MM-PH-NEWC.exe
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
--- /dev/null
+CPPFLAGS = -WF,-DOLD_GINV \
+ -WF,-DUNRES -WF,-DMPI \
+ -WF,-DSPLITELE -WF,-DISNAN \
+ -WF,-DAIX -WF,-DLANG0 -WF,-DPROCOR -WF,-DJUBL
+#-WF,-DNOXDR
+#-WF,-DPROCOR
+## -DMOMENT
+#-DCO_BIAS
+#-DCRYST_TOR
+#-DDEBUG
+
+BGLSYS = /bgl/BlueLight/ppcfloor/bglsys
+
+CC = /usr/bin/blrts_xlc
+CPPC = /usr/bin/blrts_xlc
+FC = /usr/bin/blrts_xlf90
+#-pg -g
+
+# try -qarch=440 first, then use -qarch=440d for 2nd FPU later on
+# (SIMDization requires at least -O3)
+# use -qlist -qsource with 440d and look for Parallel ASM instructions.
+#
+OPT= -I$(BGLSYS)/include -L$(BGLSYS)/lib -qarch=440d -qtune=440 -qfixed -w -qnosave
+CFLAGS= -O3 -I$(BGLSYS)/include -L$(BGLSYS)/lib -qarch=440d -qtune=440
+FFLAGS= -c -O3 ${OPT} -I./include_unres
+#
+LIBS_MPI = -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts
+LIBSF_MPI = -lmpich.rts -lfmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts
+
+FFLAGS1 = -c ${OPT} -O2
+FFLAGS2 = -c ${OPT} -O
+FFLAGSE = -c ${OPT} -O4
+
+
+BIN = ${HOME}/UNRES/bin/wham_multparm-T-procor.rts
+LIBS = ${LIBSF_MPI} ../src_Tc/xdrf/libxdrf.a
+#LIBS = ${LIBSF_MPI}
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+all: unresCSA
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+objects = \
+ wham_multparm.o \
+ cxread.o \
+ enecalc.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ rescode.o \
+ setup_var.o \
+ store_parm.o \
+ timing.o \
+ wham_calc.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+
+unresCSA: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${objects} ${objects_compar} cinfo.o ${LIBS} -o ${BIN}
+
+
+clean:
+ /bin/rm *.o
--- /dev/null
+BIN = ../bin
+CC = cc
+CFLAGS = -DAIX -c
+FC = mpxlf90 -qlistopt -qfixed -w
+OPT = -q64
+FFLAGS = -c ${OPT} -O3 -I./include_unres
+#FFLAGS = -c ${OPT} -g -C -I./include_unres
+LIBS = xdrf/libxdrf.o xdrf/ftocstr.o
+CPPFLAGS = -WF,-DMPI -WF,-DAIX -WF,-DUNRES -WF,-DSPLITELE -WF,-DPROCOR -WF,-DISNAN
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+.SUFFIXES: .c
+.c.o:
+ ${CC} ${CFLAGS} $*.c
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -o ${BIN}/wham_multparm-T-procor-c1
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+BIN = ../bin
+FC= ifort
+#OPT = -mcmodel=medium -O3 -ip -w
+OPT = -mcmodel=medium -g -CB
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DISNAN -DAMD64
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -static-intel -o ${BIN}/wham_multparm-ham_rep
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_pgi_9.0_64bit_ssh
+BIN = ../bin
+CC = cc
+FC = pgf90
+#FC = ifc
+#OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64 -C -g
+OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o -Bstatic_pgi \
+ ${LIBS} -o ${BIN}/wham_multparm-hamrep-sep
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_pgi_9.0_64bit_ssh
+BIN = ../bin
+CC = cc
+FC = pgf90
+#FC = ifc
+OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64
+#OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DCRYST_BOND -DCRYST_SC -DCRYST_THETA -DFUNCT
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o -Bstatic_pgi \
+ ${LIBS} -o ${BIN}/wham_multparm-OPTERON-SCT-sccor-oldparm
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /users/software/mpich-1.2.7p1_pgi_9.0_64bit_ssh
+BIN = ../bin
+CC = cc
+FC = pgf90
+#FC = ifc
+OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64
+#OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DCRYST_BOND -DCRYST_SC -DCRYST_THETA -DFUNCTH
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} -Bstatic_pgi cinfo.o \
+ ${LIBS} -o ${BIN}/wham_multparm-OPTERON-SCTF-sccor-oldparm
+
+clean:
+ /bin/rm *.o
--- /dev/null
+INSTALL_DIR = /usr/local/mpich-1.2.7p1_pgi64-6.2-3_ssh
+BIN = ../bin
+CC = cc
+FC = pgf90
+#FC = ifc
+OPT = -mcmodel=medium -Mlarge_arrays -fast -pc 64 -tp amd64
+#OPT = -mcmodel=medium -Mlarge_arrays -tp amd64
+#FFLAGS = ${OPT} -g -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+#FFLAGS = ${OPT} -c -C -g -I. -I./include_unres -I$(INSTALL_DIR)/include
+FFLAGS = ${OPT} -c -I. -I./include_unres -I$(INSTALL_DIR)/include
+LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xdrf/libxdrf.a
+#LIBS = -L$(INSTALL_DIR)/lib_pgi -lmpich -lpmpich -Vaxlib
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DMOMENT -DCHECKGRAD -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DCHECKGRAD -DPGI -DMYGETENV
+CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITELE -DPROCOR -DPGI -DCRYST_BOND -DCRYST_SC -DCRYST_THETA
+#CPPFLAGS = -DMPI -DLINUX -DUNRES -DPGI
+#CPPFLAGS = -DMPI -DLINUX -DUNRES
+
+.f.o:
+ ${FC} ${FFLAGS} $*.f
+
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+all: make_dbase
+
+objects = \
+ wham_multparm.o \
+ bxread.o \
+ xread.o \
+ cxread.o \
+ enecalc1.o \
+ energy_p_new.o \
+ initialize_p.o \
+ molread_zs.o \
+ openunits.o \
+ readrtns.o \
+ arcos.o \
+ cartder.o \
+ cartprint.o \
+ chainbuild.o \
+ geomout.o \
+ icant.o \
+ intcor.o \
+ int_from_cart.o \
+ make_ensemble1.o \
+ matmult.o \
+ misc.o \
+ mygetenv.o \
+ parmread.o \
+ pinorm.o \
+ printmat.o \
+ proc_proc.o \
+ rescode.o \
+ setup_var.o \
+ slices.o \
+ store_parm.o \
+ timing.o \
+ wham_calc1.o
+
+objects_compar = \
+ readrtns_compar.o \
+ readpdb.o fitsq.o contact.o \
+ elecont.o contfunc.o cont_frag.o conf_compar.o match_contact.o \
+ angnorm.o odlodc.o promienie.o qwolynes.o read_ref_str.o \
+ rmscalc.o secondary.o proc_cont.o define_pairs.o mysort.o
+
+make_dbase: ${objects} ${objects_compar}
+ cc -o compinfo compinfo.c
+ ./compinfo
+ ${FC} -c ${FFLAGS} cinfo.f
+ $(FC) ${OPT} ${objects} ${objects_compar} cinfo.o \
+ ${LIBS} -o ${BIN}/wham_multparm-OPTERON-SCTF-sccor-oldparm
+
+clean:
+ /bin/rm *.o
--- /dev/null
+a=1
+echo $a
+while [ $a -lt 10 ]
+do
+ a=`expr $a + 1`
+done
+echo $a
+b=`expr $a / 5`
+echo a=$a b=$b
--- /dev/null
+ subroutine add_angpair(ici,icj,nang_pair,iang_pair)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ integer ici,icj,nang_pair,iang_pair(2,maxres)
+ integer i,ian1,ian2
+c write (iout,*) "add_angpair: ici",ici," icj",icj,
+c & " nang_pair",nang_pair
+ ian1=ici+2
+ if (ian1.lt.4 .or. ian1.gt.nres) return
+ ian2=icj+2
+c write (iout,*) "ian1",ian1," ian2",ian2
+ if (ian2.lt.4 .or. ian2.gt.nres) return
+ do i=1,nang_pair
+ if (ian1.eq.iang_pair(1,i) .and. ian2.eq.iang_pair(2,i)) return
+ enddo
+ nang_pair=nang_pair+1
+ iang_pair(1,nang_pair)=ian1
+ iang_pair(2,nang_pair)=ian2
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine angnorm(jfrag,ishif1,ishif2,diffang_max,angn,fract,
+ & lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.VAR'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ double precision pinorm,deltang
+ logical lprn
+ if (lprn) write (iout,'(80(1h*))')
+ angn=0.0d0
+ nn = 0
+ fract = 1.0d0
+ npart = npiece(jfrag,1)
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+ if (lprn) write (iout,*) "nn4",nn4," nne",nne
+ do i=1,npart
+ nbeg = ifrag(1,i,jfrag) + 3 - ishif1
+ if (nbeg.lt.nn4) nbeg=nn4
+ nend = ifrag(2,i,jfrag) + 1 - ishif2
+ if (nend.gt.nne) nend=nne
+ if (nend.ge.nbeg) then
+ nn = nn + nend - nbeg + 1
+ if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,
+ & " nn",nn," ishift1",ishif1," ishift2",ishif2
+ if (lprn) write (iout,*) "angles"
+ longest=0
+ ll = 0
+ do j=nbeg,nend
+c deltang = pinorm(phi(j)-phi_ref(j+ishif1))
+ deltang=spherang(phi_ref(j+ishif1),theta_ref(j-1+ishif1),
+ & theta_ref(j+ishif1),phi(j),theta(j-1),theta(j))
+ if (dabs(deltang).gt.diffang_max) then
+ if (ll.gt.longest) longest = ll
+ ll = 0
+ else
+ ll=ll+1
+ endif
+ if (ll.gt.longest) longest = ll
+ if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),
+ & rad2deg*phi_ref(j+ishif1),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ longest=longest+3
+ ff = dfloat(longest)/dfloat(nend - nbeg + 4)
+ if (lprn) write (iout,*)"segment",i," longest fragment within",
+ & diffang_max*rad2deg,":",longest," fraction",ff
+ if (ff.lt.fract) fract = ff
+ endif
+ enddo
+ if (nn.gt.0) then
+ angn = angn/nn
+ else
+ angn = dwapi
+ endif
+ if (lprn) write (iout,*) "nn",nn," norm",rad2deg*angn,
+ & " fract",fract
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine angnorm2(jfrag,ishif1,ishif2,ncont,icont,lprn,
+ & diffang_max,anorm,fract)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.VAR'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ integer ncont,icont(2,ncont),longest
+ double precision anorm,diffang_max,fract
+ integer npiece_c,ifrag_c(2,maxpiece),ishift_c(maxpiece)
+ double precision pinorm
+ logical lprn
+ if (lprn) write (iout,'(80(1h*))')
+c
+c Determine the segments for which angles will be compared
+c
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+ if (lprn) write (iout,*) "nn4",nn4," nne",nne
+ npart=npiece(jfrag,1)
+ npiece_c=0
+ do i=1,npart
+c write (iout,*) "i",i," ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ if (icont(1,ncont).lt.ifrag(1,i,jfrag) .or.
+ & icont(1,1).gt.ifrag(2,i,jfrag)) goto 11
+ jstart=1
+ do while (jstart.lt.ncont .and.
+ & icont(1,jstart).lt.ifrag(1,i,jfrag))
+c write (iout,*) "jstart",jstart," icont",icont(1,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart+1
+ enddo
+c write (iout,*) "jstart",jstart," icont",icont(1,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ if (icont(1,jstart).lt.ifrag(1,i,jfrag)) goto 11
+ npiece_c=npiece_c+1
+ ic1=icont(1,jstart)
+ ifrag_c(1,npiece_c)=icont(1,jstart)
+ jend=ncont
+ do while (jend.gt.1 .and. icont(1,jend).gt.ifrag(2,i,jfrag))
+c write (iout,*) "jend",jend," icont",icont(1,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ jend=jend-1
+ enddo
+c write (iout,*) "jend",jend," icont",icont(1,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ ic2=icont(1,jend)
+ ifrag_c(2,npiece_c)=icont(1,jend)+1
+ ishift_c(npiece_c)=ishif1
+c write (iout,*) "1: i",i," jstart:",jstart," jend",jend,
+c & " ic1",ic1," ic2",ic2,
+c & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ 11 continue
+ if (ncont.eq.1 .or. icont(2,ncont).gt.icont(2,1)) then
+ idi=1
+ else
+ idi=-1
+ endif
+c write (iout,*) "idi",idi
+ if (idi.eq.1) then
+ if (icont(2,1).gt.ifrag(2,i,jfrag) .or.
+ & icont(2,ncont).lt.ifrag(1,i,jfrag)) goto 12
+ jstart=1
+ do while (jstart.lt.ncont .and.
+ & icont(2,jstart).lt.ifrag(1,i,jfrag))
+c write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart+1
+ enddo
+c write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
+ npiece_c=npiece_c+1
+ ic1=icont(2,jstart)
+ ifrag_c(2,npiece_c)=icont(2,jstart)+1
+ jend=ncont
+ do while (jend.gt.1 .and. icont(2,jend).gt.ifrag(2,i,jfrag))
+c write (iout,*) "jend",jend," icont",icont(2,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ jend=jend-1
+ enddo
+c write (iout,*) "jend",jend," icont",icont(2,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ else if (idi.eq.-1) then
+ if (icont(2,ncont).gt.ifrag(2,i,jfrag) .or.
+ & icont(2,1).lt.ifrag(1,i,jfrag)) goto 12
+ jstart=ncont
+ do while (jstart.gt.ncont .and.
+ & icont(2,jstart).lt.ifrag(1,i,jfrag))
+c write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ jstart=jstart-1
+ enddo
+c write (iout,*) "jstart",jstart," icont",icont(2,jstart),
+c & " ifrag",ifrag(1,i,jfrag)
+ if (icont(2,jstart).lt.ifrag(1,i,jfrag)) goto 12
+ npiece_c=npiece_c+1
+ ic1=icont(2,jstart)
+ ifrag_c(2,npiece_c)=icont(2,jstart)+1
+ jend=1
+ do while (jend.lt.ncont .and.
+ & icont(2,jend).gt.ifrag(2,i,jfrag))
+c write (iout,*) "jend",jend," icont",icont(2,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ jend=jend+1
+ enddo
+c write (iout,*) "jend",jend," icont",icont(2,jend),
+c & " ifrag",ifrag(2,i,jfrag)
+ endif
+ ic2=icont(2,jend)
+ if (ic2.lt.ic1) then
+ iic = ic1
+ ic1 = ic2
+ ic2 = iic
+ endif
+c write (iout,*) "2: i",i," ic1",ic1," ic2",ic2,
+c & " jstart:",jstart," jend",jend,
+c & " ifrag",ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ ifrag_c(1,npiece_c)=ic1
+ ifrag_c(2,npiece_c)=ic2+1
+ ishift_c(npiece_c)=ishif2
+ 12 continue
+ enddo
+ if (lprn) then
+ write (iout,*) "Before merge: npiece_c",npiece_c
+ do i=1,npiece_c
+ write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
+ enddo
+ endif
+c
+c Merge overlapping segments (e.g., avoid splitting helices)
+c
+ i=1
+ do while (i .lt. npiece_c)
+ if (ishift_c(i).eq.ishift_c(i+1) .and.
+ & ifrag_c(2,i).gt.ifrag_c(1,i+1)) then
+ ifrag_c(2,i)=ifrag_c(2,i+1)
+ do j=i+1,npiece_c
+ ishift_c(j)=ishift_c(j+1)
+ ifrag_c(1,j)=ifrag_c(1,j+1)
+ ifrag_c(2,j)=ifrag_c(2,j+1)
+ enddo
+ npiece_c=npiece_c-1
+ else
+ i=i+1
+ endif
+ enddo
+ if (lprn) then
+ write (iout,*) "After merge: npiece_c",npiece_c
+ do i=1,npiece_c
+ write (iout,*) ifrag_c(1,i),ifrag_c(2,i),ishift_c(i)
+ enddo
+ endif
+c
+c Compare angles
+c
+ angn=0.0d0
+ anorm=0
+ nn = 0
+ fract = 1.0d0
+ npart = npiece_c
+ do i=1,npart
+ ishifc=ishift_c(i)
+ nbeg = ifrag_c(1,i) + 3 - ishifc
+ if (nbeg.lt.nn4) nbeg=nn4
+ nend = ifrag_c(2,i) - ishifc + 1
+ if (nend.gt.nne) nend=nne
+ if (nend.ge.nbeg) then
+ nn = nn + nend - nbeg + 1
+ if (lprn) write (iout,*) "i=",i," nbeg",nbeg," nend",nend,
+ & " nn",nn," ishifc",ishifc
+ if (lprn) write (iout,*) "angles"
+ longest=0
+ ll = 0
+ do j=nbeg,nend
+c deltang = pinorm(phi(j)-phi_ref(j+ishifc))
+ deltang=spherang(phi_ref(j+ishifc),theta_ref(j-1+ishifc),
+ & theta_ref(j+ishifc),phi(j),theta(j-1),theta(j))
+ if (dabs(deltang).gt.diffang_max) then
+ if (ll.gt.longest) longest = ll
+ ll = 0
+ else
+ ll=ll+1
+ endif
+ if (ll.gt.longest) longest = ll
+ if (lprn) write (iout,'(i5,3f10.5)')j,rad2deg*phi(j),
+ & rad2deg*phi_ref(j+ishifc),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ longest=longest+3
+ ff = dfloat(longest)/dfloat(nend - nbeg + 4)
+ if (lprn) write (iout,*)"segment",i," longest fragment within",
+ & diffang_max*rad2deg,":",longest," fraction",ff
+ if (ff.lt.fract) fract = ff
+ endif
+ enddo
+ if (nn.gt.0) anorm = angn/nn
+ if (lprn) write (iout,*) "nn",nn," norm",anorm," fract:",fract
+ return
+ end
+c-------------------------------------------------------------------------
+ double precision function angnorm1(nang_pair,iang_pair,lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.VAR'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ logical lprn
+ integer nang_pair,iang_pair(2,maxres)
+ double precision pinorm
+ angn=0.0d0
+ if (lprn) write (iout,'(80(1h*))')
+ if (lprn) write (iout,*) "nang_pair",nang_pair
+ if (lprn) write (iout,*) "angles"
+ do j=1,nang_pair
+ ia1 = iang_pair(1,j)
+ ia2 = iang_pair(2,j)
+c deltang = pinorm(phi(ia1)-phi_ref(ia2))
+ deltang=spherang(phi_ref(ia2),theta_ref(ia2-1),
+ & theta_ref(ia2),phi(ia2),theta(ia2-1),theta(ia2))
+ if (lprn) write (iout,'(3i5,3f10.5)')j,ia1,ia2,rad2deg*phi(ia1),
+ & rad2deg*phi_ref(ia2),rad2deg*deltang
+ angn=angn+dabs(deltang)
+ enddo
+ if (lprn)
+ &write (iout,*)"nang_pair",nang_pair," angn",rad2deg*angn/nang_pair
+ angnorm1 = angn/nang_pair
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine angnorm12(diff)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.VAR'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ double precision pinorm
+ diff=0.0d0
+ nn4 = nstart_sup+3
+ nne = min0(nend_sup,nres)
+c do j=nn4-1,nne
+c diff = diff+rad2deg*dabs(pinorm(theta(j)-theta_ref(j)))
+c enddo
+ do j=nn4,nne
+c diff = diff+rad2deg*dabs(pinorm(phi(j)-phi_ref(j)))
+ diff=diff+spherang(phi_ref(j),theta_ref(j-1),
+ & theta_ref(j),phi(j),theta(j-1),theta(j))
+ enddo
+ return
+ end
+c--------------------------------------------------------------------------------
+ double precision function spherang(gam1,theta11,theta12,
+ & gam2,theta21,theta22)
+ implicit none
+ double precision gam1,theta11,theta12,gam2,theta21,theta22,
+ & x1,x2,xmed,f1,f2,fmed
+ double precision tolx /1.0d-4/, tolf /1.0d-4/
+ double precision sumcos
+ double precision arcos,pinorm,sumangp
+ integer it,maxit /100/
+c Calculate the difference of the angles of two superposed 4-redidue fragments
+c
+c O P
+c \ /
+c O'--C--C
+c \
+c P'
+c
+c The fragment O'-C-C-P' is rotated by angle fi about the C-C axis
+c to achieve the minimum difference between the O'-C-O and P-C-P angles;
+c the sum of these angles is the difference returned by the function.
+c
+c 4/28/04 AL
+c If thetas match, take the difference of gamma and exit.
+ if (dabs(theta11-theta12).lt.tolx
+ & .and. dabs(theta21-theta22).lt.tolx) then
+ spherang=dabs(pinorm(gam2-gam1))
+ return
+ endif
+c If the gammas are the same, take the difference of thetas and exit.
+ x1=0.0d0
+ x2=0.5d0*pinorm(gam2-gam1)
+ if (dabs(x2) .lt. tolx) then
+ spherang=dabs(theta11-theta21)+dabs(theta12-theta22)
+ return
+ else if (x2.lt.0.0d0) then
+ x1=x2
+ x2=0.0d0
+ endif
+c Else apply regula falsi method to compute optimum overlap of the terminal Calphas
+ f1=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x1)
+ f2=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,x2)
+ do it=1,maxit
+ xmed=x1-f1*(x2-x1)/(f2-f1)
+ fmed=sumangp(gam1,theta11,theta12,gam2,theta21,theta22,xmed)
+c write (*,*) 'it',it,' xmed ',xmed,' fmed ',fmed
+ if ( (dabs(xmed-x1).lt.tolx .or. dabs(x2-xmed).lt.tolx)
+ & .and. dabs(fmed).lt.tolf ) then
+ x1=xmed
+ f1=fmed
+ goto 10
+ else if ( fmed*f1.lt.0.0d0 ) then
+ x2=xmed
+ f2=fmed
+ else
+ x1=xmed
+ f1=fmed
+ endif
+ enddo
+ 10 continue
+ spherang=arcos(dcos(theta11)*dcos(theta12)
+ & +dsin(theta11)*dsin(theta12)*dcos(x1))+
+ & arcos(dcos(theta21)*dcos(theta22)+
+ & dsin(theta21)*dsin(theta22)*dcos(gam2-gam1+x1))
+ return
+ end
+c--------------------------------------------------------------------------------
+ double precision function sumangp(gam1,theta11,theta12,gam2,
+ & theta21,theta22,fi)
+ implicit none
+ double precision gam1,theta11,theta12,gam2,theta21,theta22,fi,
+ & cost11,cost12,cost21,cost22,sint11,sint12,sint21,sint22,cosd1,
+ & cosd2
+c derivarive of the sum of the difference of the angles of a 4-residue fragment.
+ double precision arcos
+ cost11=dcos(theta11)
+ cost12=dcos(theta12)
+ cost21=dcos(theta21)
+ cost22=dcos(theta22)
+ sint11=dsin(theta11)
+ sint12=dsin(theta12)
+ sint21=dsin(theta21)
+ sint22=dsin(theta22)
+ cosd1=cost11*cost12+sint11*sint12*dcos(fi)
+ cosd2=cost21*cost22+sint21*sint22*dcos(gam2-gam1+fi)
+ sumangp=sint11*sint12*dsin(fi)/dsqrt(1.0d0-cosd1*cosd1)
+ & +sint21*sint22*dsin(gam2-gam1+fi)/dsqrt(1.0d0-cosd2*cosd2)
+ return
+ end
--- /dev/null
+ FUNCTION ARCOS(X)
+ implicit real*8 (a-h,o-z)
+ include 'COMMON.GEO'
+ IF (DABS(X).LT.1.0D0) GOTO 1
+ ARCOS=0.5D0*(PI+DSIGN(1.0D0,X)*PI)
+ RETURN
+ 1 ARCOS=DACOS(X)
+ RETURN
+ END
--- /dev/null
+ subroutine bxread(nazwa,islice,ii,jj,kk,ll,mm,iR,ib,iparm)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.GEO"
+ include "COMMON.ENEPS"
+ include "COMMON.PROT"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.SBRIDGE"
+ real*4 csingle(3,maxres2)
+ character*64 nazwa,bprotfile_temp
+ character*3 liczba
+ integer i,is,ie,j,ii,jj,k,kk,l,ll,mm,if
+ integer nrec,nlines,iscor,islice
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ double precision rmsdev,energia(0:max_ene),efree,eini,temp
+ double precision prop(maxQ)
+ integer ntot_all(0:maxprocs-1)
+ integer iparm,ib,iib,ir,nprop,nthr,nrec_slice
+ double precision etot,time
+ logical lerr
+ nrec_slice=(rec_end(iR,ib,iparm)-rec_start(iR,ib,iparm)+1)/nslice
+ is=rec_start(iR,ib,iparm)+(islice-1)*nrec_slice
+ ie=rec_start(iR,ib,iparm)+islice*nrec_slice-1
+ write (iout,*) "bxread: islice",islice," nslice",nslice,
+ & " nrec_slice",nrec_slice
+ write (iout,*) "is",is," ie",ie,"rec_start",
+ & rec_start(iR,ib,iparm)," rec_end",rec_end(iR,ib,iparm)
+ do i=is,ie
+ read(ientin,rec=i+1,err=101)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,(prop(j),j=1,nQ),iscor
+ ii=ii+1
+ kk=kk+1
+ if (mod(kk,isampl(iparm)).eq.0) then
+ jj=jj+1
+ write(ientout,rec=jj)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,(prop(j),j=1,nQ),iR,ib,iparm
+#ifdef DEBUG
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=csingle(j,i)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ write (iout,*) "Writing conformation, record",jj
+ write (iout,*) "Cartesian coordinates"
+ write (iout,'(8f10.5)') ((c(j,i),j=1,3),i=1,nres)
+ write (iout,'(8f10.5)') ((c(j,i+nres),j=1,3),i=nnt,nct)
+ write (iout,*) "Internal coordinates"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+ write (iout,'(f10.5,i5)') rmsdev,iscor
+#endif
+ endif
+ enddo
+ 101 continue
+ close(ientin)
+ write (iout,*) ii," conformations read from DA file ",
+ & nazwa(:ilen(nazwa))
+ write (iout,*) kk," conformations read so far, slice",islice
+ write (iout,*) jj," conformations stored so far, slice",islice
+
+ return
+ end
--- /dev/null
+ subroutine cartder
+ implicit real*8 (a-h,o-z)
+***********************************************************************
+* This subroutine calculates the derivatives of the consecutive virtual
+* bond vectors and the SC vectors in the virtual-bond angles theta and
+* virtual-torsional angles phi, as well as the derivatives of SC vectors
+* in the angles alpha and omega, describing the location of a side chain
+* in its local coordinate system.
+*
+* The derivatives are stored in the following arrays:
+*
+* DDCDV - the derivatives of virtual-bond vectors DC in theta and phi.
+* The structure is as follows:
+*
+* dDC(x,2)/dT(3),...,dDC(z,2)/dT(3),0, 0, 0
+* dDC(x,3)/dT(4),...,dDC(z,3)/dT(4),dDC(x,3)/dP(4),dDC(y,4)/dP(4),dDC(z,4)/dP(4)
+* . . . . . . . . . . . . . . . . . .
+* dDC(x,N-1)/dT(4),...,dDC(z,N-1)/dT(4),dDC(x,N-1)/dP(4),dDC(y,N-1)/dP(4),dDC(z,N-1)/dP(4)
+* .
+* .
+* .
+* dDC(x,N-1)/dT(N),...,dDC(z,N-1)/dT(N),dDC(x,N-1)/dP(N),dDC(y,N-1)/dP(N),dDC(z,N-1)/dP(N)
+*
+* DXDV - the derivatives of the side-chain vectors in theta and phi.
+* The structure is same as above.
+*
+* DCDS - the derivatives of the side chain vectors in the local spherical
+* andgles alph and omega:
+*
+* dX(x,2)/dA(2),dX(y,2)/dA(2),dX(z,2)/dA(2),dX(x,2)/dO(2),dX(y,2)/dO(2),dX(z,2)/dO(2)
+* dX(x,3)/dA(3),dX(y,3)/dA(3),dX(z,3)/dA(3),dX(x,3)/dO(3),dX(y,3)/dO(3),dX(z,3)/dO(3)
+* .
+* .
+* .
+* dX(x,N-1)/dA(N-1),dX(y,N-1)/dA(N-1),dX(z,N-1)/dA(N-1),dX(x,N-1)/dO(N-1),dX(y,N-1)/dO(N-1),dX(z,N-1)/dO(N-1)
+*
+* Version of March '95, based on an early version of November '91.
+*
+***********************************************************************
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ dimension drt(3,3,maxres),rdt(3,3,maxres),dp(3,3),temp(3,3),
+ & fromto(3,3,maxdim),prordt(3,3,maxres),prodrt(3,3,maxres)
+ dimension xx(3),xx1(3)
+* get the position of the jth ijth fragment of the chain coordinate system
+* in the fromto array.
+ indmat(i,j)=((2*(nres-2)-i)*(i-1))/2+j-1
+*
+* calculate the derivatives of transformation matrix elements in theta
+*
+ do i=1,nres-2
+ rdt(1,1,i)=-rt(1,2,i)
+ rdt(1,2,i)= rt(1,1,i)
+ rdt(1,3,i)= 0.0d0
+ rdt(2,1,i)=-rt(2,2,i)
+ rdt(2,2,i)= rt(2,1,i)
+ rdt(2,3,i)= 0.0d0
+ rdt(3,1,i)=-rt(3,2,i)
+ rdt(3,2,i)= rt(3,1,i)
+ rdt(3,3,i)= 0.0d0
+ enddo
+*
+* derivatives in phi
+*
+ do i=2,nres-2
+ drt(1,1,i)= 0.0d0
+ drt(1,2,i)= 0.0d0
+ drt(1,3,i)= 0.0d0
+ drt(2,1,i)= rt(3,1,i)
+ drt(2,2,i)= rt(3,2,i)
+ drt(2,3,i)= rt(3,3,i)
+ drt(3,1,i)=-rt(2,1,i)
+ drt(3,2,i)=-rt(2,2,i)
+ drt(3,3,i)=-rt(2,3,i)
+ enddo
+*
+* generate the matrix products of type r(i)t(i)...r(j)t(j)
+*
+ do i=2,nres-2
+ ind=indmat(i,i+1)
+ do k=1,3
+ do l=1,3
+ temp(k,l)=rt(k,l,i)
+ enddo
+ enddo
+ do k=1,3
+ do l=1,3
+ fromto(k,l,ind)=temp(k,l)
+ enddo
+ enddo
+ do j=i+1,nres-2
+ ind=indmat(i,j+1)
+ do k=1,3
+ do l=1,3
+ dpkl=0.0d0
+ do m=1,3
+ dpkl=dpkl+temp(k,m)*rt(m,l,j)
+ enddo
+ dp(k,l)=dpkl
+ fromto(k,l,ind)=dpkl
+ enddo
+ enddo
+ do k=1,3
+ do l=1,3
+ temp(k,l)=dp(k,l)
+ enddo
+ enddo
+ enddo
+ enddo
+*
+* Calculate derivatives.
+*
+ ind1=0
+ do i=1,nres-2
+ ind1=ind1+1
+*
+* Derivatives of DC(i+1) in theta(i+2)
+*
+ do j=1,3
+ do k=1,2
+ dpjk=0.0D0
+ do l=1,3
+ dpjk=dpjk+prod(j,l,i)*rdt(l,k,i)
+ enddo
+ dp(j,k)=dpjk
+ prordt(j,k,i)=dp(j,k)
+ enddo
+ dp(j,3)=0.0D0
+ dcdv(j,ind1)=vbl*dp(j,1)
+ enddo
+*
+* Derivatives of SC(i+1) in theta(i+2)
+*
+ xx1(1)=-0.5D0*xloc(2,i+1)
+ xx1(2)= 0.5D0*xloc(1,i+1)
+ do j=1,3
+ xj=0.0D0
+ do k=1,2
+ xj=xj+r(j,k,i)*xx1(k)
+ enddo
+ xx(j)=xj
+ enddo
+ do j=1,3
+ rj=0.0D0
+ do k=1,3
+ rj=rj+prod(j,k,i)*xx(k)
+ enddo
+ dxdv(j,ind1)=rj
+ enddo
+*
+* Derivatives of SC(i+1) in theta(i+3). The have to be handled differently
+* than the other off-diagonal derivatives.
+*
+ do j=1,3
+ dxoiij=0.0D0
+ do k=1,3
+ dxoiij=dxoiij+dp(j,k)*xrot(k,i+2)
+ enddo
+ dxdv(j,ind1+1)=dxoiij
+ enddo
+cd print *,ind1+1,(dxdv(j,ind1+1),j=1,3)
+*
+* Derivatives of DC(i+1) in phi(i+2)
+*
+ do j=1,3
+ do k=1,3
+ dpjk=0.0
+ do l=2,3
+ dpjk=dpjk+prod(j,l,i)*drt(l,k,i)
+ enddo
+ dp(j,k)=dpjk
+ prodrt(j,k,i)=dp(j,k)
+ enddo
+ dcdv(j+3,ind1)=vbl*dp(j,1)
+ enddo
+*
+* Derivatives of SC(i+1) in phi(i+2)
+*
+ xx(1)= 0.0D0
+ xx(3)= xloc(2,i+1)*r(2,2,i)+xloc(3,i+1)*r(2,3,i)
+ xx(2)=-xloc(2,i+1)*r(3,2,i)-xloc(3,i+1)*r(3,3,i)
+ do j=1,3
+ rj=0.0D0
+ do k=2,3
+ rj=rj+prod(j,k,i)*xx(k)
+ enddo
+ dxdv(j+3,ind1)=-rj
+ enddo
+*
+* Derivatives of SC(i+1) in phi(i+3).
+*
+ do j=1,3
+ dxoiij=0.0D0
+ do k=1,3
+ dxoiij=dxoiij+dp(j,k)*xrot(k,i+2)
+ enddo
+ dxdv(j+3,ind1+1)=dxoiij
+ enddo
+*
+* Calculate the derivatives of DC(i+1) and SC(i+1) in theta(i+3) thru
+* theta(nres) and phi(i+3) thru phi(nres).
+*
+ do j=i+1,nres-2
+ ind1=ind1+1
+ ind=indmat(i+1,j+1)
+cd print *,'i=',i,' j=',j,' ind=',ind,' ind1=',ind1
+ do k=1,3
+ do l=1,3
+ tempkl=0.0D0
+ do m=1,2
+ tempkl=tempkl+prordt(k,m,i)*fromto(m,l,ind)
+ enddo
+ temp(k,l)=tempkl
+ enddo
+ enddo
+cd print '(9f8.3)',((fromto(k,l,ind),l=1,3),k=1,3)
+cd print '(9f8.3)',((prod(k,l,i),l=1,3),k=1,3)
+cd print '(9f8.3)',((temp(k,l),l=1,3),k=1,3)
+* Derivatives of virtual-bond vectors in theta
+ do k=1,3
+ dcdv(k,ind1)=vbl*temp(k,1)
+ enddo
+cd print '(3f8.3)',(dcdv(k,ind1),k=1,3)
+* Derivatives of SC vectors in theta
+ do k=1,3
+ dxoijk=0.0D0
+ do l=1,3
+ dxoijk=dxoijk+temp(k,l)*xrot(l,j+2)
+ enddo
+ dxdv(k,ind1+1)=dxoijk
+ enddo
+*
+*--- Calculate the derivatives in phi
+*
+ do k=1,3
+ do l=1,3
+ tempkl=0.0D0
+ do m=1,3
+ tempkl=tempkl+prodrt(k,m,i)*fromto(m,l,ind)
+ enddo
+ temp(k,l)=tempkl
+ enddo
+ enddo
+ do k=1,3
+ dcdv(k+3,ind1)=vbl*temp(k,1)
+ enddo
+ do k=1,3
+ dxoijk=0.0D0
+ do l=1,3
+ dxoijk=dxoijk+temp(k,l)*xrot(l,j+2)
+ enddo
+ dxdv(k+3,ind1+1)=dxoijk
+ enddo
+ enddo
+ enddo
+*
+* Derivatives in alpha and omega:
+*
+ do i=2,nres-1
+ dsci=dsc(itype(i))
+ alphi=alph(i)
+ omegi=omeg(i)
+cd print *,'i=',i,' dsci=',dsci,' alphi=',alphi,' omegi=',omegi
+ cosalphi=dcos(alphi)
+ sinalphi=dsin(alphi)
+ cosomegi=dcos(omegi)
+ sinomegi=dsin(omegi)
+ temp(1,1)=-dsci*sinalphi
+ temp(2,1)= dsci*cosalphi*cosomegi
+ temp(3,1)=-dsci*cosalphi*sinomegi
+ temp(1,2)=0.0D0
+ temp(2,2)=-dsci*sinalphi*sinomegi
+ temp(3,2)=-dsci*sinalphi*cosomegi
+ theta2=pi-0.5D0*theta(i+1)
+ cost2=dcos(theta2)
+ sint2=dsin(theta2)
+ jjj=0
+cd print *,((temp(l,k),l=1,3),k=1,2)
+ do j=1,2
+ xp=temp(1,j)
+ yp=temp(2,j)
+ xxp= xp*cost2+yp*sint2
+ yyp=-xp*sint2+yp*cost2
+ zzp=temp(3,j)
+ xx(1)=xxp
+ xx(2)=yyp*r(2,2,i-1)+zzp*r(2,3,i-1)
+ xx(3)=yyp*r(3,2,i-1)+zzp*r(3,3,i-1)
+ do k=1,3
+ dj=0.0D0
+ do l=1,3
+ dj=dj+prod(k,l,i-1)*xx(l)
+ enddo
+ dxds(jjj+k,i)=dj
+ enddo
+ jjj=jjj+3
+ enddo
+ enddo
+ return
+ end
+
--- /dev/null
+ subroutine cartprint
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ write (iout,100)
+ do i=1,nres
+ write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),
+ & c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
+ enddo
+ 100 format (//' alpha-carbon coordinates ',
+ & ' centroid coordinates'/
+ 1 ' ', 6X,'X',11X,'Y',11X,'Z',
+ & 10X,'X',11X,'Y',11X,'Z')
+ 110 format (a,'(',i3,')',6f12.5)
+ return
+ end
--- /dev/null
+ subroutine chainbuild
+C
+C Build the virtual polypeptide chain. Side-chain centroids are moveable.
+C As of 2/17/95.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn = .false.
+C
+C Define the origin and orientation of the coordinate system and locate the
+C first three CA's and SC(2).
+C
+ call orig_frame
+*
+* Build the alpha-carbon chain.
+*
+ do i=4,nres
+ call locate_next_res(i)
+ enddo
+C
+C First and last SC must coincide with the corresponding CA.
+C
+ do j=1,3
+ dc(j,nres+1)=0.0D0
+ dc_norm(j,nres+1)=0.0D0
+ dc(j,nres+nres)=0.0D0
+ dc_norm(j,nres+nres)=0.0D0
+ c(j,nres+1)=c(j,1)
+ c(j,nres+nres)=c(j,nres)
+ enddo
+*
+* Temporary diagnosis
+*
+ if (lprn) then
+
+ call cartprint
+ write (iout,'(/a)') 'Recalculated internal coordinates'
+ do i=2,nres-1
+ do j=1,3
+ c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
+ enddo
+ be=0.0D0
+ if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
+ be1=rad2deg*beta(nres+i,i,maxres2,i+1)
+ alfai=0.0D0
+ if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
+ write (iout,1212) restyp(itype(i)),i,dist(i-1,i),
+ & alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,maxres2),be1
+ enddo
+ 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
+
+ endif
+
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine orig_frame
+C
+C Define the origin and orientation of the coordinate system and locate
+C the first three atoms.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ cost=dcos(theta(3))
+ sint=dsin(theta(3))
+ t(1,1,1)=-cost
+ t(1,2,1)=-sint
+ t(1,3,1)= 0.0D0
+ t(2,1,1)=-sint
+ t(2,2,1)= cost
+ t(2,3,1)= 0.0D0
+ t(3,1,1)= 0.0D0
+ t(3,2,1)= 0.0D0
+ t(3,3,1)= 1.0D0
+ r(1,1,1)= 1.0D0
+ r(1,2,1)= 0.0D0
+ r(1,3,1)= 0.0D0
+ r(2,1,1)= 0.0D0
+ r(2,2,1)= 1.0D0
+ r(2,3,1)= 0.0D0
+ r(3,1,1)= 0.0D0
+ r(3,2,1)= 0.0D0
+ r(3,3,1)= 1.0D0
+ do i=1,3
+ do j=1,3
+ rt(i,j,1)=t(i,j,1)
+ enddo
+ enddo
+ do i=1,3
+ do j=1,3
+ prod(i,j,1)=0.0D0
+ prod(i,j,2)=t(i,j,1)
+ enddo
+ prod(i,i,1)=1.0D0
+ enddo
+ c(1,1)=0.0D0
+ c(2,1)=0.0D0
+ c(3,1)=0.0D0
+ c(1,2)=vbld(2)
+ c(2,2)=0.0D0
+ c(3,2)=0.0D0
+ dc(1,1)=vbld(2)
+ dc(2,1)=0.0D0
+ dc(3,1)=0.0D0
+ dc_norm(1,1)=1.0D0
+ dc_norm(2,1)=0.0D0
+ dc_norm(3,1)=0.0D0
+ do j=1,3
+ dc_norm(j,2)=prod(j,1,2)
+ dc(j,2)=vbld(3)*prod(j,1,2)
+ c(j,3)=c(j,2)+dc(j,2)
+ enddo
+ call locate_side_chain(2)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine locate_next_res(i)
+C
+C Locate CA(i) and SC(i-1)
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+C
+C Define the rotation matrices corresponding to CA(i)
+C
+#ifdef OSF
+ theti=theta(i)
+ icrc=0
+ call proc_proc(theti,icrc)
+ if(icrc.eq.1)theti=100.0
+ phii=phi(i)
+ icrc=0
+ call proc_proc(phii,icrc)
+ if(icrc.eq.1)phii=180.0
+#else
+ theti=theta(i)
+ phii=phi(i)
+#endif
+ cost=dcos(theti)
+ sint=dsin(theti)
+ cosphi=dcos(phii)
+ sinphi=dsin(phii)
+* Define the matrices of the rotation about the virtual-bond valence angles
+* theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
+* program), R(i,j,k), and, the cumulative matrices of rotation RT
+ t(1,1,i-2)=-cost
+ t(1,2,i-2)=-sint
+ t(1,3,i-2)= 0.0D0
+ t(2,1,i-2)=-sint
+ t(2,2,i-2)= cost
+ t(2,3,i-2)= 0.0D0
+ t(3,1,i-2)= 0.0D0
+ t(3,2,i-2)= 0.0D0
+ t(3,3,i-2)= 1.0D0
+ r(1,1,i-2)= 1.0D0
+ r(1,2,i-2)= 0.0D0
+ r(1,3,i-2)= 0.0D0
+ r(2,1,i-2)= 0.0D0
+ r(2,2,i-2)=-cosphi
+ r(2,3,i-2)= sinphi
+ r(3,1,i-2)= 0.0D0
+ r(3,2,i-2)= sinphi
+ r(3,3,i-2)= cosphi
+ rt(1,1,i-2)=-cost
+ rt(1,2,i-2)=-sint
+ rt(1,3,i-2)=0.0D0
+ rt(2,1,i-2)=sint*cosphi
+ rt(2,2,i-2)=-cost*cosphi
+ rt(2,3,i-2)=sinphi
+ rt(3,1,i-2)=-sint*sinphi
+ rt(3,2,i-2)=cost*sinphi
+ rt(3,3,i-2)=cosphi
+ call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
+ do j=1,3
+ dc_norm(j,i-1)=prod(j,1,i-1)
+ dc(j,i-1)=vbld(i)*prod(j,1,i-1)
+ c(j,i)=c(j,i-1)+dc(j,i-1)
+ enddo
+cd print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
+C
+C Now calculate the coordinates of SC(i-1)
+C
+ call locate_side_chain(i-1)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine locate_side_chain(i)
+C
+C Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ dimension xx(3)
+
+c dsci=dsc(itype(i))
+c dsci_inv=dsc_inv(itype(i))
+ dsci=vbld(i+nres)
+ dsci_inv=vbld_inv(i+nres)
+#ifdef OSF
+ alphi=alph(i)
+ omegi=omeg(i)
+c detecting NaNQ
+ icrc=0
+ call proc_proc(alphi,icrc)
+ if(icrc.eq.1)alphi=100.0
+ icrc=0
+ call proc_proc(omegi,icrc)
+ if(icrc.eq.1)omegi=-100.0
+#else
+ alphi=alph(i)
+ omegi=omeg(i)
+#endif
+ cosalphi=dcos(alphi)
+ sinalphi=dsin(alphi)
+ cosomegi=dcos(omegi)
+ sinomegi=dsin(omegi)
+ xp= dsci*cosalphi
+ yp= dsci*sinalphi*cosomegi
+ zp=-dsci*sinalphi*sinomegi
+* Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
+* X-axis aligned with the vector DC(*,i)
+ theta2=pi-0.5D0*theta(i+1)
+ cost2=dcos(theta2)
+ sint2=dsin(theta2)
+ xx(1)= xp*cost2+yp*sint2
+ xx(2)=-xp*sint2+yp*cost2
+ xx(3)= zp
+cd print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i)),i,
+cd & xp,yp,zp,(xx(k),k=1,3)
+ do j=1,3
+ xloc(j,i)=xx(j)
+ enddo
+* Bring the SC vectors to the common coordinate system.
+ xx(1)=xloc(1,i)
+ xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
+ xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
+ do j=1,3
+ xrot(j,i)=xx(j)
+ enddo
+ do j=1,3
+ rj=0.0D0
+ do k=1,3
+ rj=rj+prod(j,k,i-1)*xx(k)
+ enddo
+ dc(j,nres+i)=rj
+ dc_norm(j,nres+i)=rj*dsci_inv
+ c(j,nres+i)=c(j,i)+rj
+ enddo
+ return
+ end
--- /dev/null
+ subroutine chainbuild
+C
+C Build the virtual polypeptide chain. Side-chain centroids are moveable.
+C As of 2/17/95.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn = .false.
+C
+C Define the origin and orientation of the coordinate system and locate the
+C first three CA's and SC(2).
+C
+ call orig_frame
+*
+* Build the alpha-carbon chain.
+*
+ do i=4,nres
+ call locate_next_res(i)
+ enddo
+C
+C First and last SC must coincide with the corresponding CA.
+C
+ do j=1,3
+ dc(j,nres+1)=0.0D0
+ dc_norm(j,nres+1)=0.0D0
+ dc(j,nres+nres)=0.0D0
+ dc_norm(j,nres+nres)=0.0D0
+ c(j,nres+1)=c(j,1)
+ c(j,nres+nres)=c(j,nres)
+ enddo
+*
+* Temporary diagnosis
+*
+ if (lprn) then
+
+ call cartprint
+ write (iout,'(/a)') 'Recalculated internal coordinates'
+ do i=2,nres-1
+ do j=1,3
+ c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
+ enddo
+ be=0.0D0
+ if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
+ be1=rad2deg*beta(nres+i,i,maxres2,i+1)
+ alfai=0.0D0
+ if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
+ write (iout,1212) restyp(itype(i)),i,dist(i-1,i),
+ & alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,maxres2),be1
+ enddo
+ 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
+
+ endif
+
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine orig_frame
+C
+C Define the origin and orientation of the coordinate system and locate
+C the first three atoms.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ cost=dcos(theta(3))
+ sint=dsin(theta(3))
+ t(1,1,1)=-cost
+ t(1,2,1)=-sint
+ t(1,3,1)= 0.0D0
+ t(2,1,1)=-sint
+ t(2,2,1)= cost
+ t(2,3,1)= 0.0D0
+ t(3,1,1)= 0.0D0
+ t(3,2,1)= 0.0D0
+ t(3,3,1)= 1.0D0
+ r(1,1,1)= 1.0D0
+ r(1,2,1)= 0.0D0
+ r(1,3,1)= 0.0D0
+ r(2,1,1)= 0.0D0
+ r(2,2,1)= 1.0D0
+ r(2,3,1)= 0.0D0
+ r(3,1,1)= 0.0D0
+ r(3,2,1)= 0.0D0
+ r(3,3,1)= 1.0D0
+ do i=1,3
+ do j=1,3
+ rt(i,j,1)=t(i,j,1)
+ enddo
+ enddo
+ do i=1,3
+ do j=1,3
+ prod(i,j,1)=0.0D0
+ prod(i,j,2)=t(i,j,1)
+ enddo
+ prod(i,i,1)=1.0D0
+ enddo
+ c(1,1)=0.0D0
+ c(2,1)=0.0D0
+ c(3,1)=0.0D0
+ c(1,2)=vbld(2)
+ c(2,2)=0.0D0
+ c(3,2)=0.0D0
+ dc(1,1)=vbld(2)
+ dc(2,1)=0.0D0
+ dc(3,1)=0.0D0
+ dc_norm(1,1)=1.0D0
+ dc_norm(2,1)=0.0D0
+ dc_norm(3,1)=0.0D0
+ do j=1,3
+ dc_norm(j,2)=prod(j,1,2)
+ dc(j,2)=vbld(3)*prod(j,1,2)
+ c(j,3)=c(j,2)+dc(j,2)
+ enddo
+ call locate_side_chain(2)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine locate_next_res(i)
+C
+C Locate CA(i) and SC(i-1)
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+C
+C Define the rotation matrices corresponding to CA(i)
+C
+ theti=theta(i)
+ phii=phi(i)
+ cost=dcos(theti)
+ sint=dsin(theti)
+ cosphi=dcos(phii)
+ sinphi=dsin(phii)
+* Define the matrices of the rotation about the virtual-bond valence angles
+* theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
+* program), R(i,j,k), and, the cumulative matrices of rotation RT
+ t(1,1,i-2)=-cost
+ t(1,2,i-2)=-sint
+ t(1,3,i-2)= 0.0D0
+ t(2,1,i-2)=-sint
+ t(2,2,i-2)= cost
+ t(2,3,i-2)= 0.0D0
+ t(3,1,i-2)= 0.0D0
+ t(3,2,i-2)= 0.0D0
+ t(3,3,i-2)= 1.0D0
+ r(1,1,i-2)= 1.0D0
+ r(1,2,i-2)= 0.0D0
+ r(1,3,i-2)= 0.0D0
+ r(2,1,i-2)= 0.0D0
+ r(2,2,i-2)=-cosphi
+ r(2,3,i-2)= sinphi
+ r(3,1,i-2)= 0.0D0
+ r(3,2,i-2)= sinphi
+ r(3,3,i-2)= cosphi
+ rt(1,1,i-2)=-cost
+ rt(1,2,i-2)=-sint
+ rt(1,3,i-2)=0.0D0
+ rt(2,1,i-2)=sint*cosphi
+ rt(2,2,i-2)=-cost*cosphi
+ rt(2,3,i-2)=sinphi
+ rt(3,1,i-2)=-sint*sinphi
+ rt(3,2,i-2)=cost*sinphi
+ rt(3,3,i-2)=cosphi
+ call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
+ do j=1,3
+ dc_norm(j,i-1)=prod(j,1,i-1)
+ dc(j,i-1)=vbld(i)*prod(j,1,i-1)
+ c(j,i)=c(j,i-1)+dc(j,i-1)
+ enddo
+cd print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
+C
+C Now calculate the coordinates of SC(i-1)
+C
+ call locate_side_chain(i-1)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine locate_side_chain(i)
+C
+C Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ dimension xx(3)
+
+c dsci=dsc(itype(i))
+c dsci_inv=dsc_inv(itype(i))
+ dsci=vbld(i+nres)
+ dsci_inv=vbld_inv(i+nres)
+ alphi=alph(i)
+ omegi=omeg(i)
+ cosalphi=dcos(alphi)
+ sinalphi=dsin(alphi)
+ cosomegi=dcos(omegi)
+ sinomegi=dsin(omegi)
+ xp= dsci*cosalphi
+ yp= dsci*sinalphi*cosomegi
+ zp=-dsci*sinalphi*sinomegi
+* Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
+* X-axis aligned with the vector DC(*,i)
+ theta2=pi-0.5D0*theta(i+1)
+ cost2=dcos(theta2)
+ sint2=dsin(theta2)
+ xx(1)= xp*cost2+yp*sint2
+ xx(2)=-xp*sint2+yp*cost2
+ xx(3)= zp
+cd print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i)),i,
+cd & xp,yp,zp,(xx(k),k=1,3)
+ do j=1,3
+ xloc(j,i)=xx(j)
+ enddo
+* Bring the SC vectors to the common coordinate system.
+ xx(1)=xloc(1,i)
+ xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
+ xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
+ do j=1,3
+ xrot(j,i)=xx(j)
+ enddo
+ do j=1,3
+ rj=0.0D0
+ do k=1,3
+ rj=rj+prod(j,k,i-1)*xx(k)
+ enddo
+ dc(j,nres+i)=rj
+ dc_norm(j,nres+i)=rj*dsci_inv
+ c(j,nres+i)=c(j,i)+rj
+ enddo
+ return
+ end
--- /dev/null
+#include <stdio.h>
+#include <sys/utsname.h>
+#include <sys/types.h>
+#include <time.h>
+#include <string.h>
+
+main()
+{
+FILE *in, *in1, *out;
+int i,j,k,iv1,iv2,iv3;
+char *p1,buf[500],buf1[500],buf2[100],buf3[100];
+struct utsname Name;
+time_t Tp;
+
+in=fopen("cinfo.f","r");
+out=fopen("cinfo.f.new","w");
+if (fgets(buf,498,in) != NULL)
+ fprintf(out,"C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C\n");
+if (fgets(buf,498,in) != NULL)
+ sscanf(&buf[1],"%d %d %d",&iv1,&iv2,&iv3);
+iv3++;
+fprintf(out,"C %d %d %d\n",iv1,iv2,iv3);
+fprintf(out," subroutine cinfo\n");
+fprintf(out," include 'COMMON.IOUNITS'\n");
+fprintf(out," write(iout,*)'++++ Compile info ++++'\n");
+fprintf(out," write(iout,*)'Version %d.%-d build %d'\n",iv1,iv2,iv3);
+uname(&Name);
+time(&Tp);
+system("whoami > tmptmp");
+in1=fopen("tmptmp","r");
+if (fscanf(in1,"%s",buf1) != EOF)
+{
+p1=ctime(&Tp);
+p1[strlen(p1)-1]='\0';
+fprintf(out," write(iout,*)'compiled %s'\n",p1);
+fprintf(out," write(iout,*)'compiled by %s@%s'\n",buf1,Name.nodename);
+fprintf(out," write(iout,*)'OS name: %s '\n",Name.sysname);
+fprintf(out," write(iout,*)'OS release: %s '\n",Name.release);
+fprintf(out," write(iout,*)'OS version:',\n");
+fprintf(out," & ' %s '\n",Name.version);
+fprintf(out," write(iout,*)'flags:'\n");
+}
+system("rm tmptmp");
+fclose(in1);
+in1=fopen("Makefile","r");
+while(fgets(buf,498,in1) != NULL)
+ {
+ if((p1=strchr(buf,'=')) != NULL && buf[0] != '#')
+ {
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ else
+ {
+ while(buf[strlen(buf)-1]=='\\')
+ {
+ strcat(buf,"\\");
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ if (fgets(buf,498,in1) != NULL)
+ buf[strlen(buf)-1]='\0';
+ if(strlen(buf) > 49)
+ {
+ buf[47]='\0';
+ strcat(buf,"...");
+ }
+ }
+ }
+
+ fprintf(out," write(iout,*)'%s'\n",buf);
+ }
+ }
+fprintf(out," write(iout,*)'++++ End of compile info ++++'\n");
+fprintf(out," return\n");
+fprintf(out," end\n");
+fclose(out);
+fclose(in1);
+fclose(in);
+system("mv cinfo.f.new cinfo.f");
+}
--- /dev/null
+ subroutine conf_compar(jcon,lprn,print_class)
+ implicit real*8 (a-h,o-z)
+#ifdef MPI
+ include "mpif.h"
+#endif
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.PEPTCONT'
+ include 'COMMON.CONTACTS1'
+ include 'COMMON.HEADER'
+ include 'COMMON.FREE'
+ include 'COMMON.ENERGIES'
+#ifdef MPI
+ include 'COMMON.MPI'
+#endif
+ integer ilen
+ external ilen
+ logical lprn,print_class
+ integer ncont_frag(mmaxfrag),
+ & icont_frag(2,maxcont,mmaxfrag),ncontsc,
+ & icontsc(1,maxcont),nsccont_frag(mmaxfrag),
+ & isccont_frag(2,maxcont,mmaxfrag)
+ integer isecstr(maxres)
+ integer itemp(maxfrag)
+ character*4 liczba
+ double precision Epot
+c print *,"Enter conf_compar",jcon
+ call angnorm12(rmsang)
+c Level 1: check secondary and supersecondary structure
+ call elecont(lprn,ncont,icont,nnt,nct)
+ call secondary2(lprn,.false.,ncont,icont,isecstr)
+ call contact(lprn,ncontsc,icontsc,nnt,nct)
+ if (lprn) write(iout,*) "Assigning electrostatic contacts"
+ call contacts_between_fragments(lprn,3,ncont,icont,ncont_frag,
+ & icont_frag)
+ if (lprn) write(iout,*) "Assigning sidechain contacts"
+ call contacts_between_fragments(lprn,3,ncontsc,icontsc,
+ & nsccont_frag,isccont_frag)
+ do i=1,nlevel
+ do j=1,isnfrag(nlevel+1)
+ iclass(j,i)=0
+ enddo
+ enddo
+ do j=1,nfrag(1)
+ ind = icant(j,j)
+ if (lprn) then
+ write (iout,'(80(1h=))')
+ write (iout,*) "Level",1," fragment",j
+ write (iout,'(80(1h=))')
+ endif
+ rmsfrag(j,1)=rmscalc(0,1,j,jcon,lprn)
+c Compare electrostatic contacts in the current conf with that in the native
+c structure.
+ if (lprn) write (iout,*)
+ & "Comparing electrostatic contact map and local structure"
+ ncnat=ncont_frag_ref(ind)
+c write (iout,*) "before match_contact:",nc_fragm(j,1),
+c & nc_req_setf(j,1)
+ call match_secondary(j,isecstr,nsec_match,lprn)
+ if (lprn) write (iout,*) "Fragment",j," nsec_match",
+ & nsec_match," length",len_frag(j,1)," min_len",
+ & frac_sec*len_frag(j,1)
+ if (nsec_match.lt.frac_sec*len_frag(j,1)) then
+ iclass(j,1)=0
+ if (lprn) write (iout,*) "Fragment",j,
+ & " has incorrect secondary structure"
+ else
+ iclass(j,1)=1
+ if (lprn) write (iout,*) "Fragment",j,
+ & " has correct secondary structure"
+ endif
+ if (ielecont(j,1).gt.0) then
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,
+ & ncont_frag_ref(ind),icont_frag_ref(1,1,ind),
+ & ncont_frag(ind),icont_frag(1,1,ind),
+ & j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
+ & nc_req_setf(j,1),istruct(j),.true.,lprn)
+ else if (isccont(j,1).gt.0) then
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,
+ & nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),
+ & nsccont_frag(ind),isccont_frag(1,1,ind),
+ & j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
+ & nc_req_setf(j,1),istruct(j),.true.,lprn)
+ else if (iloc(j).gt.0) then
+c write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,
+ & 0,icont_frag_ref(1,1,ind),
+ & ncont_frag(ind),icont_frag(1,1,ind),
+ & j,n_shift(1,j,1),n_shift(2,j,1),nc_fragm(j,1),
+ & 0,istruct(j),.true.,lprn)
+c write (iout,*) "n_shif",n_shift(1,j,1),n_shift(2,j,1)
+ else
+ ishif=0
+ nc_match=1
+ endif
+ if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2
+ ishif=ishif1
+ qfrag(j,1)=qwolynes(1,j)
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (lprn) write (iout,*) "ishift",ishif," nc_match",nc_match
+c write (iout,*) "j",j," ishif",ishif," rms",rmsfrag(j,1)
+ if (irms(j,1).gt.0) then
+ if (rmsfrag(j,1).le.rmscutfrag(1,j,1)) then
+ iclass_rms=2
+ ishifft_rms=0
+ else
+ ishiff=0
+ rms=1.0d2
+ iclass_rms=0
+ do while (rms.gt.rmscutfrag(1,j,1) .and.
+ & ishiff.lt.n_shift(1,j,1))
+ ishiff=ishiff+1
+ rms=rmscalc(-ishiff,1,j,jcon,lprn)
+c write(iout,*)"jcon,i,j,ishiff",jcon,i,j,-ishiff,
+c & " rms",rms," rmscut",rmscutfrag(1,j,1)
+ if (lprn) write (iout,*) "rms",rmsfrag(j,1)
+ if (rms.gt.rmscutfrag(1,j,1)) then
+ rms=rmscalc(ishiff,1,j,jcon,lprn)
+c write (iout,*) "jcon,1,j,ishiff",jcon,1,j,ishiff,
+c & " rms",rms
+ endif
+ if (lprn) write (iout,*) "rms",rmsfrag(j,1)
+ enddo
+c write (iout,*) "After loop: rms",rms,
+c & " rmscut",rmscutfrag(1,j,1)
+c write (iout,*) "iclass_rms",iclass_rms
+ if (rms.le.rmscutfrag(1,j,1)) then
+ ishifft_rms=ishiff
+ rmsfrag(j,1)=rms
+ iclass_rms=1
+ endif
+c write (iout,*) "iclass_rms",iclass_rms
+ endif
+c write (iout,*) "ishif",ishif
+ if (iabs(ishifft_rms).gt.iabs(ishif)) ishif=ishifft_rms
+ else
+ iclass_rms=1
+ endif
+c write (iout,*) "ishif",ishif," iclass",iclass(j,1),
+c & " iclass_rms",iclass_rms
+ if (nc_match.gt.0 .and. iclass_rms.gt.0) then
+ if (ishif.eq.0) then
+ iclass(j,1)=iclass(j,1)+6
+ else
+ iclass(j,1)=iclass(j,1)+2
+ endif
+ endif
+ ncont_nat(1,j,1)=nc_match
+ ncont_nat(2,j,1)=ncon_match
+ ishifft(j,1)=ishif
+c write (iout,*) "iclass",iclass(j,1)
+ enddo
+c Next levels: Check arrangements of elementary fragments.
+ do i=2,nlevel
+ do j=1,nfrag(i)
+ if (i .eq. 2) ind = icant(ipiece(1,j,i),ipiece(2,j,i))
+ if (lprn) then
+ write (iout,'(80(1h=))')
+ write (iout,*) "Level",i," fragment",j
+ write (iout,'(80(1h=))')
+ endif
+c If an elementary fragment doesn't exist, don't check higher hierarchy levels.
+ do k=1,npiece(j,i)
+ ik=ipiece(k,j,i)
+ if (iclass(ik,1).eq.0) then
+ iclass(j,i)=0
+ goto 12
+ endif
+ enddo
+ if (i.eq.2 .and. ielecont(j,i).gt.0) then
+ iclass_con=0
+ ishifft_con=0
+ if (lprn) write (iout,*)
+ & "Comparing electrostatic contact map: fragments",
+ & ipiece(1,j,i),ipiece(2,j,i)," ind",ind
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,
+ & ncont_frag_ref(ind),icont_frag_ref(1,1,ind),
+ & ncont_frag(ind),icont_frag(1,1,ind),
+ & j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),
+ & nc_req_setf(j,i),2,.false.,lprn)
+ ishif=ishif1
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (nc_match.gt.0) then
+ if (ishif.eq.0) then
+ iclass_con=2
+ else
+ iclass_con=1
+ endif
+ endif
+ ncont_nat(1,j,i)=nc_match
+ ncont_nat(2,j,i)=ncon_match
+ ishifft_con=ishif
+ else if (i.eq.2 .and. isccont(j,i).gt.0) then
+ iclass_con=0
+ ishifft_con=0
+ if (lprn) write (iout,*)
+ & "Comparing sidechain contact map: fragments",
+ & ipiece(1,j,i),ipiece(2,j,i)," ind",ind
+ call match_contact(ishif1,ishif2,nc_match,ncon_match,
+ & nsccont_frag_ref(ind),isccont_frag_ref(1,1,ind),
+ & nsccont_frag(ind),isccont_frag(1,1,ind),
+ & j,n_shift(1,j,i),n_shift(2,j,i),nc_fragm(j,i),
+ & nc_req_setf(j,i),2,.false.,lprn)
+ ishif=ishif1
+ if (iabs(ishif2).gt.iabs(ishif1)) ishif=ishif2
+ if (nc_match.gt.0) then
+ if (ishif.eq.0) then
+ iclass_con=2
+ else
+ iclass_con=1
+ endif
+ endif
+ ncont_nat(1,j,i)=nc_match
+ ncont_nat(2,j,i)=ncon_match
+ ishifft_con=ishif
+ else if (i.eq.2) then
+ iclass_con=2
+ ishifft_con=0
+ endif
+ if (i.eq.2) qfrag(j,2)=qwolynes(2,j)
+ if (lprn) write (iout,*)
+ & "Comparing rms: fragments",
+ & (ipiece(k,j,i),k=1,npiece(j,i))
+ rmsfrag(j,i)=rmscalc(0,i,j,jcon,lprn)
+ if (irms(j,i).gt.0) then
+ iclass_rms=0
+ ishifft_rms=0
+ if (lprn) write (iout,*) "rms",rmsfrag(j,i)
+c write (iout,*) "i",i," j",j," rmsfrag",rmsfrag(j,i),
+c & " rmscutfrag",rmscutfrag(1,j,i)
+ if (rmsfrag(j,i).le.rmscutfrag(1,j,i)) then
+ iclass_rms=2
+ ishifft_rms=0
+ else
+ ishif=0
+ rms=1.0d2
+ do while (rms.gt.rmscutfrag(1,j,i) .and.
+ & ishif.lt.n_shift(1,j,i))
+ ishif=ishif+1
+ rms=rmscalc(-ishif,i,j,jcon,lprn)
+c print *,"jcon,i,j,ishif",jcon,i,j,-ishif," rms",rms
+ if (lprn) write (iout,*) "rms",rmsfrag(j,i)
+ if (rms.gt.rmscutfrag(1,j,i)) then
+ rms=rmscalc(ishif,i,j,jcon,lprn)
+c print *,"jcon,i,j,ishif",jcon,i,j,ishif," rms",rms
+ endif
+ if (lprn) write (iout,*) "rms",rms
+ enddo
+ if (rms.le.rmscutfrag(1,j,i)) then
+ ishifft_rms=ishif
+ rmsfrag(j,i)=rms
+ iclass_rms=1
+ endif
+ endif
+ endif
+ if (irms(j,i).eq.0 .and. ielecont(j,i).eq.0 .and.
+ & isccont(j,i).eq.0 ) then
+ write (iout,*) "Error: no measure of comparison specified:",
+ & " level",i," part",j
+ stop
+ endif
+ if (lprn)
+ & write (iout,*) "iclass_con",iclass_con," iclass_rms",iclass_rms
+ if (i.eq.2) then
+ iclass(j,i) = min0(iclass_con,iclass_rms)
+ if (iabs(ishifft_rms).gt.iabs(ishifft_con)) then
+ ishifft(j,i)=ishifft_rms
+ else
+ ishifft(j,i)=ishifft_con
+ endif
+ else if (i.gt.2) then
+ iclass(j,i) = iclass_rms
+ ishifft(j,i)= ishifft_rms
+ endif
+ 12 continue
+ enddo
+ enddo
+ rms_nat=rmsnat(jcon)
+ qnat=qwolynes(0,0)
+C Compute the structural class
+ iscor=0
+ IF (.NOT. BINARY) THEN
+ do i=1,nlevel
+ IF (I.EQ.1) THEN
+ do j=1,nfrag(i)
+ itemp(j)=iclass(j,i)
+ enddo
+ do kk=-1,1
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-kk*nfrag(i)-j
+ iex = 2**idig
+ im=mod(itemp(j),2)
+ itemp(j)=itemp(j)/2
+c write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+c & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ enddo
+ ELSE
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-j
+ iex = 2**idig
+ if (iclass(j,i).gt.0) then
+ im=1
+ else
+ im=0
+ endif
+c write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+c & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ do j=1,nfrag(i)
+ idig = 2*isnfrag(nlevel+1)-2*isnfrag(i)-nfrag(i)-j
+ iex = 2**idig
+ if (iclass(j,i).gt.1) then
+ im=1
+ else
+ im=0
+ endif
+c write (iout,*) "i",i," j",j," idig",idig," iex",iex,
+c & " iclass",iclass(j,i)," im",im
+ iscor=iscor+im*iex
+ enddo
+ ENDIF
+ enddo
+ iscore=iscor
+ ENDIF
+ if (print_class) then
+#ifdef MPI
+ write(istat,'(i6,$)') jcon+indstart(me)-1
+ write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),
+ & -entfac(jcon)
+#else
+ write(istat,'(i6,$)') jcon
+ write (istat,'(f10.2,$)') (potE(jcon,k),k=1,nParmSet),
+ & -entfac(jcon)
+#endif
+ write (istat,'(f8.3,2f6.3,$)')
+ & rms_nat,qnat,rmsang/(nres-3)
+ do j=1,nlevel
+ write(istat,'(1x,$,20(i3,$))')
+ & (ncont_nat(1,k,j),k=1,nfrag(j))
+ if (j.lt.3) then
+ write(istat,'(1x,$,20(f5.1,f5.2$))')
+ & (rmsfrag(k,j),qfrag(k,j),k=1,nfrag(j))
+ else
+ write(istat,'(1x,$,20(f5.1$))')
+ & (rmsfrag(k,j),k=1,nfrag(j))
+ endif
+ write(istat,'(1x,$,20(i1,$))')
+ & (iclass(k,j),k=1,nfrag(j))
+ enddo
+ if (binary) then
+ write (istat,'(" ",$)')
+ do j=1,nlevel
+ write (istat,'(100(i1,$))')(iclass(k,j),
+ & k=1,nfrag(j))
+ if (j.lt.nlevel) write(iout,'(".",$)')
+ enddo
+ write (istat,*)
+ else
+ write (istat,'(i10)') iscore
+ endif
+ endif
+ RETURN
+ END
--- /dev/null
+ subroutine contacts_between_fragments(lprint,is,ncont,icont,
+ & ncont_interfrag,icont_interfrag)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ integer icont(2,maxcont),ncont_interfrag(mmaxfrag),
+ & icont_interfrag(2,maxcont,mmaxfrag)
+ logical OK1,OK2,lprint
+c Determine the contacts that occur within a fragment and between fragments.
+ do i=1,nfrag(1)
+ do j=1,i
+ ind = icant(i,j)
+ nc=0
+c write (iout,*) "i",i,(ifrag(1,k,i),ifrag(2,k,i)
+c & ,k=1,npiece(i,1))
+c write (iout,*) "j",j,(ifrag(1,k,j),ifrag(2,k,j)
+c & ,k=1,npiece(j,1))
+c write (iout,*) "ncont",ncont
+ do k=1,ncont
+ ic1=icont(1,k)
+ ic2=icont(2,k)
+ OK1=.false.
+ l=0
+ do while (.not.OK1 .and. l.lt.npiece(j,1))
+ l=l+1
+ OK1=ic1.ge.ifrag(1,l,j)-is .and.
+ & ic1.le.ifrag(2,l,j)+is
+ enddo
+ OK2=.false.
+ l=0
+ do while (.not.OK2 .and. l.lt.npiece(i,1))
+ l=l+1
+ OK2=ic2.ge.ifrag(1,l,i)-is .and.
+ & ic2.le.ifrag(2,l,i)+is
+ enddo
+c write(iout,*) "k",k," ic1",ic1," ic2",ic2," OK1",OK1,
+c & " OK2",OK2
+ if (OK1.and.OK2) then
+ nc=nc+1
+ icont_interfrag(1,nc,ind)=ic1
+ icont_interfrag(2,nc,ind)=ic2
+c write (iout,*) "nc",nc," ic1",ic1," ic2",ic2
+ endif
+ enddo
+ ncont_interfrag(ind)=nc
+c do k=1,ncont_interfrag(ind)
+c i1=icont_interfrag(1,k,ind)
+c i2=icont_interfrag(2,k,ind)
+c it1=itype(i1)
+c it2=itype(i2)
+c write (iout,'(i3,2x,a,i4,2x,a,i4)')
+c & i,restyp(it1),i1,restyp(it2),i2
+c enddo
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,*) "Contacts within fragments:"
+ do i=1,nfrag(1)
+ write (iout,*) "Fragment",i," (",(ifrag(1,k,i),
+ & ifrag(2,k,i),k=1,npiece(i,1)),")"
+ ind=icant(i,i)
+ do k=1,ncont_interfrag(ind)
+ i1=icont_interfrag(1,k,ind)
+ i2=icont_interfrag(2,k,ind)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ enddo
+ write (iout,*)
+ write (iout,*) "Contacts between fragments:"
+ do i=1,nfrag(1)
+ do j=1,i-1
+ ind = icant(i,j)
+ write (iout,*) "Fragments",i," (",(ifrag(1,k,i),
+ & ifrag(2,k,i),k=1,npiece(i,1)),") and",j," (",
+ & (ifrag(1,k,j),ifrag(2,k,j),k=1,npiece(j,1)),")"
+ write (iout,*) "Number of contacts",
+ & ncont_interfrag(ind)
+ ind=icant(i,j)
+ do k=1,ncont_interfrag(ind)
+ i1=icont_interfrag(1,k,ind)
+ i2=icont_interfrag(2,k,ind)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ enddo
+ enddo
+ endif
+ return
+ end
--- /dev/null
+ subroutine contact(lprint,ncont,icont,ist,ien)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTPAR'
+ include 'COMMON.LOCAL'
+ integer ist,ien,kkk,iti,itj,itypi,itypj,i1,i2,it1,it2
+ real*8 csc,dist
+ real*8 cscore(maxcont),omt1(maxcont),omt2(maxcont),omt12(maxcont),
+ & ddsc(maxcont),ddla(maxcont),ddlb(maxcont)
+ integer ncont,icont(2,maxcont)
+ real*8 u,v,a(3),b(3),dla,dlb
+ logical lprint
+ ncont=0
+ kkk=3
+ if (lprint) then
+ do i=1,nres
+ write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),
+ & c(3,i),dc(1,nres+i),dc(2,nres+i),dc(3,nres+i),
+ & dc_norm(1,nres+i),dc_norm(2,nres+i),dc_norm(3,nres+i)
+ enddo
+ endif
+ 110 format (a,'(',i3,')',9f8.3)
+ do i=ist,ien-kkk
+ iti=itype(i)
+ do j=i+kkk,ien
+ itj=itype(j)
+ itypi=iti
+ itypj=itj
+ xj = c(1,nres+j)-c(1,nres+i)
+ yj = c(2,nres+j)-c(2,nres+i)
+ zj = c(3,nres+j)-c(3,nres+i)
+ dxi = dc_norm(1,nres+i)
+ dyi = dc_norm(2,nres+i)
+ dzi = dc_norm(3,nres+i)
+ dxj = dc_norm(1,nres+j)
+ dyj = dc_norm(2,nres+j)
+ dzj = dc_norm(3,nres+j)
+ do k=1,3
+ a(k)=dc(k,nres+i)
+ b(k)=dc(k,nres+j)
+ enddo
+c write (iout,*) (a(k),k=1,3),(b(k),k=1,3)
+ if (icomparfunc.eq.1) then
+ call contfunc(csc,iti,itj)
+ else if (icomparfunc.eq.2) then
+ call scdist(csc,iti,itj)
+ else if (icomparfunc.eq.3 .or. icomparfunc.eq.5) then
+ csc = dist(nres+i,nres+j)
+ else if (icomparfunc.eq.4) then
+ call odlodc(c(1,i),c(1,j),a,b,u,v,dla,dlb,csc)
+ else
+ write (*,*) "Error - Unknown sidechain contact function"
+ write (iout,*) "Error - Unknown sidechain contact function"
+ endif
+ if (csc.lt.sc_cutoff(iti,itj)) then
+c write(iout,*) "i",i," j",j," dla",dla,dsc(iti),
+c & " dlb",dlb,dsc(itj)," csc",csc,sc_cutoff(iti,itj),
+c & dxi,dyi,dzi,dxi**2+dyi**2+dzi**2,
+c & dxj,dyj,dzj,dxj**2+dyj**2+dzj**2,om1,om2,om12,
+c & xj,yj,zj
+c write(iout,*)'egb',itypi,itypj,chi1,chi2,chip1,chip2,
+c & sig0ij,rij,rrij,om1,om2,om12,chiom1,chiom2,chiom12,
+c & chipom1,chipom2,chipom12,sig,eps2rt,rij_shift,e2,evdw,
+c & csc
+ ncont=ncont+1
+ cscore(ncont)=csc
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ omt1(ncont)=om1
+ omt2(ncont)=om2
+ omt12(ncont)=om12
+ ddsc(ncont)=1.0d0/rij
+ ddla(ncont)=dla
+ ddlb(ncont)=dlb
+ endif
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') 'Contact map:'
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)')
+ & i,restyp(it1),i1,restyp(it2),i2,cscore(i),
+ & sc_cutoff(it1,it2),ddsc(i),ddla(i),ddlb(i),
+ & omt1(i),omt2(i),omt12(i)
+ enddo
+ endif
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function contact_fract(ncont,ncont_ref,
+ & icont,icont_ref)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ integer i,j,nmatch
+ integer ncont,ncont_ref,icont(2,maxcont),icont_ref(2,maxcont)
+ nmatch=0
+c print *,'ncont=',ncont,' ncont_ref=',ncont_ref
+c write (iout,'(20i4)') (icont_ref(1,i),i=1,ncont_ref)
+c write (iout,'(20i4)') (icont_ref(2,i),i=1,ncont_ref)
+c write (iout,'(20i4)') (icont(1,i),i=1,ncont)
+c write (iout,'(20i4)') (icont(2,i),i=1,ncont)
+ do i=1,ncont
+ do j=1,ncont_ref
+ if (icont(1,i).eq.icont_ref(1,j) .and.
+ & icont(2,i).eq.icont_ref(2,j)) nmatch=nmatch+1
+ enddo
+ enddo
+c print *,' nmatch=',nmatch
+c contact_fract=dfloat(nmatch)/dfloat(max0(ncont,ncont_ref))
+ contact_fract=dfloat(nmatch)/dfloat(ncont_ref)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine pept_cont(lprint,ncont,icont)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ integer ncont,icont(2,maxcont)
+ integer i,j,k,kkk,i1,i2,it1,it2
+ logical lprint
+ real*8 dist
+ real*8 rcomp /5.5d0/
+ ncont=0
+ kkk=0
+ print *,'Entering pept_cont: nnt=',nnt,' nct=',nct
+ do i=nnt,nct-3
+ do k=1,3
+ c(k,2*nres+1)=0.5d0*(c(k,i)+c(k,i+1))
+ enddo
+ do j=i+2,nct-1
+ do k=1,3
+ c(k,2*nres+2)=0.5d0*(c(k,j)+c(k,j+1))
+ enddo
+ if (dist(2*nres+1,2*nres+2).lt.rcomp) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ endif
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') 'PP contact map:'
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ endif
+ return
+ end
--- /dev/null
+ subroutine contfunc(cscore,itypi,itypj)
+C
+C This subroutine calculates the contact function based on
+C the Gay-Berne potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CONTPAR'
+ include 'COMMON.CALC'
+ integer expon /6/
+C
+ sig0ij=sig_comp(itypi,itypj)
+ chi1=chi_comp(itypi,itypj)
+ chi2=chi_comp(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip_comp(itypi,itypj)
+ chip2=chip_comp(itypj,itypi)
+ chip12=chip1*chip2
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of the contact function
+ erij(1)=xj*rij
+ erij(2)=yj*rij
+ erij(3)=zj*rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ chiom12=chi12*om12
+c print *,'egb',itypi,itypj,chi1,chi2,chip1,chip2,
+c & sig0ij,
+c & rij,rrij,om1,om2,om12
+C Calculate eps1(om12)
+ faceps1=1.0D0-om12*chiom12
+ faceps1_inv=1.0D0/faceps1
+ eps1=dsqrt(faceps1_inv)
+C Following variable is eps1*deps1/dom12
+ eps1_om12=faceps1_inv*chiom12
+C Calculate sigma(om1,om2,om12)
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
+ sigsq=1.0D0-facsig*faceps1_inv
+C Calculate eps2 and its derivatives in om1, om2, and om12.
+ chipom1=chip1*om1
+ chipom2=chip2*om2
+ chipom12=chip12*om12
+ facp=1.0D0-om12*chipom12
+ facp_inv=1.0D0/facp
+ facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
+C Following variable is the square root of eps2
+ eps2rt=1.0D0-facp1*facp_inv
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+sig0ij
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D1
+ cscore = -dlog(evdw+1.0d-6)
+ return
+ endif
+ rij_shift=1.0D0/rij_shift
+ e2=(rij_shift*sig0ij)**expon
+ evdw=dabs(eps1*eps2rt**2*e2)
+ if (evdw.gt.1.0d1) evdw = 1.0d1
+ cscore = -dlog(evdw+1.0d-6)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine scdist(cscore,itypi,itypj)
+C
+C This subroutine calculates the contact distance
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CONTPAR'
+ include 'COMMON.CALC'
+C
+ chi1=chi_comp(itypi,itypj)
+ chi2=chi_comp(itypj,itypi)
+ chi12=chi1*chi2
+ rrij=xj*xj+yj*yj+zj*zj
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of the contact function
+ erij(1)=xj/rij
+ erij(2)=yj/rij
+ erij(3)=zj/rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ chiom12=chi12*om12
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ cscore=dsqrt(rrij+chi1**2+chi2**2+2*rij*(chiom2-chiom1)-2*chiom12)
+ return
+ end
--- /dev/null
+ subroutine cxread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm,*)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+#ifdef MPI
+ include "mpif.h"
+ include "COMMON.MPI"
+#endif
+ integer MaxTraj
+ parameter (MaxTraj=2050)
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.HEADER'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.PROTFILES'
+ include 'COMMON.OBCINKA'
+ include 'COMMON.FREE'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.PROT'
+ character*64 nazwa,bprotfile_temp
+ real*4 rtime,rpotE,ruconst,rt_bath,rprop(maxQ)
+ double precision time
+ integer iret,itmp,itraj,ntraj
+ real xoord(3,maxres2+2),prec
+ integer nstep(0:MaxTraj-1)
+ integer ilen
+ external ilen
+ integer ii,jj(maxslice),kk(maxslice),ll(maxslice),mm(maxslice)
+ integer is(MaxSlice),ie(MaxSlice),nrec_slice
+ double precision ts(MaxSlice),te(MaxSlice),time_slice
+ integer slice
+ logical conf_check
+ character*4 lt_bath
+ character*256 pdbfilename
+ character*50 tytul
+ call set_slices(is,ie,ts,te,iR,ib,iparm)
+
+ do i=1,nQ
+ rprop(i)=0.0d0
+ enddo
+ do i=0,MaxTraj-1
+ nstep(i)=0
+ enddo
+ ntraj=0
+ it=0
+ iret=1
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfopen_(ixdrf,nazwa, "r", iret)
+#else
+ call xdrfopen(ixdrf,nazwa, "r", iret)
+#endif
+ if (iret.eq.0) return1
+
+ islice1=1
+ call opentmp(islice1,ientout,bprotfile_temp)
+c print *,"bumbum"
+ do while (iret.gt.0)
+
+#if (defined(AIX) && !defined(JUBL))
+#ifdef DEBUG
+ write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
+ call xdrffloat_(ixdrf, rtime, iret)
+ call xdrffloat_(ixdrf, rpotE, iret)
+#ifdef DEBUG
+ write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
+ call flush(iout)
+ call xdrffloat_(ixdrf, ruconst, iret)
+ call xdrffloat_(ixdrf, rt_bath, iret)
+ call xdrfint_(ixdrf, nss, iret)
+#ifdef DEBUG
+ write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
+ do j=1,nss
+ call xdrfint_(ixdrf, ihpb(j), iret)
+ call xdrfint_(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrfint_(ixdrf, nprop, iret)
+ if (umbrella(iparm) .or. read_iset(iparm) .or. hamil_rep)
+ & call xdrfint(ixdrf, iset, iret)
+ do i=1,nprop
+ call xdrffloat_(ixdrf, rprop(i), iret)
+ enddo
+#else
+#ifdef DEBUG
+ write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
+ call xdrffloat(ixdrf, rtime, iret)
+ call xdrffloat(ixdrf, rpotE, iret)
+#ifdef DEBUG
+ write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
+ call flush(iout)
+ call xdrffloat(ixdrf, ruconst, iret)
+ call xdrffloat(ixdrf, rt_bath, iret)
+ call xdrfint(ixdrf, nss, iret)
+#ifdef DEBUG
+ write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrfint(ixdrf, nprop, iret)
+c write (iout,*) "nprop",nprop
+ if (it.gt.0 .and. nprop.ne.nprop_prev) then
+ write (iout,*) "Warning previous nprop",nprop_prev,
+ & " current",nprop
+ nprop=nprop_prev
+ else
+ nprop_prev=nprop
+ endif
+ call flush(iout)
+ if (umbrella(iparm) .or. read_iset(iparm) .or. hamil_rep)
+ & call xdrfint(ixdrf, iset, iret)
+ do i=1,nprop
+ call xdrffloat(ixdrf, rprop(i), iret)
+ enddo
+#endif
+ if (iret.eq.0) exit
+ itraj=mod(it,totraj(iR,iparm))
+ if (iset.eq.0) iset = 1
+ call flush(iout)
+ it=it+1
+ if (itraj.gt.ntraj) ntraj=itraj
+ nstep(itraj)=nstep(itraj)+1
+c rprop(2)=dsqrt(rprop(2))
+c rprop(3)=dsqrt(rprop(3))
+#ifdef DEBUG
+ write (iout,*) "umbrella ",umbrella
+ write (iout,*) rtime,rpotE,rt_bath,nss,
+ & (ihpb(j),jhpb(j),j=1,nss),(rprop(j),j=1,nprop)
+ write (iout,*) "nprop",nprop," iset",iset," myparm",myparm
+ call flush(iout)
+#endif
+ prec=10000.0
+
+ itmp=0
+#if (defined(AIX) && !defined(JUBL))
+ call xdrf3dfcoord_(ixdrf, xoord, itmp, prec, iret)
+#else
+ call xdrf3dfcoord(ixdrf, xoord, itmp, prec, iret)
+#endif
+#ifdef DEBUG
+ write (iout,'(10f8.3)') ((xoord(j,i),j=1,3),i=1,itmp)
+#endif
+ if (iret.eq.0) exit
+ if (itmp .ne. nres + nct - nnt + 1) then
+ write (iout,*) "Error: inconsistent sizes",itmp,nres+nct-nnt+1
+ call flush(iout)
+ exit
+ endif
+
+ time=rtime
+c write (iout,*) "calling slice"
+c call flush(iout)
+ islice=slice(nstep(itraj),time,is,ie,ts,te)
+c write (iout,*) "islice",islice
+c call flush(iout)
+
+ do i=1,nres
+ do j=1,3
+ c(j,i)=xoord(j,i)
+ enddo
+ enddo
+ do i=1,nct-nnt+1
+ do j=1,3
+ c(j,i+nres+nnt-1)=xoord(j,i+nres)
+ enddo
+ enddo
+
+ if (islice.gt.0 .and. islice.le.nslice .and. (.not.separate_parset
+ & .or. iset.eq.myparm)) then
+ ii=ii+1
+ kk(islice)=kk(islice)+1
+ mm(islice)=mm(islice)+1
+ if (mod(nstep(itraj),isampl(iparm)).eq.0 .and.
+ & conf_check(ll(islice)+1,1)) then
+ if (replica(iparm)) then
+ rt_bath=1.0d0/(rt_bath*1.987D-3)
+ do i=1,nT_h(iparm)
+ if (abs(real(beta_h(i,iparm))-rt_bath).lt.1.0e-4) then
+ iib = i
+ goto 22
+ endif
+ enddo
+ 22 continue
+ if (i.gt.nT_h(iparm)) then
+ write (iout,*) "Error - temperature of conformation",
+ & ii,1.0d0/(rt_bath*1.987D-3),
+ & " does not match any of the list"
+ write (iout,*)
+ & 1.0d0/(rt_bath*1.987D-3),
+ & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+ call flush(iout)
+c exit
+c call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
+ ii=ii-1
+ kk(islice)=kk(islice)-1
+ mm(islice)=mm(islice)-1
+ goto 112
+ endif
+ else
+ iib = ib
+ endif
+
+ efree=0.0d0
+ jj(islice)=jj(islice)+1
+ if (umbrella(iparm)) then
+ snk(iset,iib,iparm,islice)=snk(iset,iib,iparm,islice)+1
+ else if (hamil_rep) then
+ snk(1,iib,iparm,islice)=snk(1,iib,iparm,islice)+1
+ else
+ snk(iR,iib,iparm,islice)=snk(iR,iib,iparm,islice)+1
+ endif
+ ll(islice)=ll(islice)+1
+#ifdef DEBUG
+ write (iout,*) "Writing conformation, record",ll(islice)
+ write (iout,*) "ib",ib," iib",iib
+ write (iout,*) "ntraj",ntraj," itraj",itraj,
+ & " nstep",nstep(itraj)
+ write (iout,*) "pote",rpotE," time",rtime
+c if (replica(iparm)) then
+c write (iout,*) "TEMP",1.0d0/(rt_bath*1.987D-3)
+c write (iout,*) "TEMP list"
+c write (iout,*)
+c & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+c endif
+ write (iout,*) "iparm",iparm," ib",ib," iR",iR," nQ",nQ
+c write (iout,*) "nres",nres," nnt",nnt," nct",nct," nss",nss
+c write (iout,*) "length",nres*4+(nct-nnt+1)*4+4+2*nss*4
+ call flush(iout)
+#endif
+ if (islice.ne.islice1) then
+c write (iout,*) "islice",islice," islice1",islice1
+ close(ientout)
+c write (iout,*) "Closing file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+ call opentmp(islice,ientout,bprotfile_temp)
+c write (iout,*) "Opening file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+ islice1=islice
+ endif
+ if (umbrella(iparm)) then
+ write(ientout,rec=ll(islice))
+ & ((xoord(l,k),l=1,3),k=1,nres),
+ & ((xoord(l,k),l=1,3),k=nres+1,nres+nct-nnt+1),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & rpotE+0.0d0,efree,rmsdev,(rprop(i)+0.0d0,i=1,nQ),
+ & iset,iib,iparm
+ else if (hamil_rep) then
+ write(ientout,rec=ll(islice))
+ & ((xoord(l,k),l=1,3),k=1,nres),
+ & ((xoord(l,k),l=1,3),k=nres+1,nres+nct-nnt+1),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & rpotE+0.0d0,efree,rmsdev,(rprop(i)+0.0d0,i=1,nQ),
+ & iR,iib,iset
+ else
+ write(ientout,rec=ll(islice))
+ & ((xoord(l,k),l=1,3),k=1,nres),
+ & ((xoord(l,k),l=1,3),k=nres+1,nres+nct-nnt+1),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & rpotE+0.0d0,efree,rmsdev,(rprop(i)+0.0d0,i=1,nQ),
+ & iR,iib,iparm
+ endif
+#ifdef PDBOUT
+#ifdef MPI
+ if (me.eq.Master) then
+#endif
+ write (iout,*) "PDBOUT"
+ write (iout,*) "temperature",1.0d0/(rt_bath*1.987D-3)
+ call flush(iout)
+ write (lt_bath,'(f4.0)') 1.0d0/(rt_bath*1.987D-3)
+ write (iout,*) "lt_bath ",lt_bath
+ pdbfilename=prefix(:ilen(prefix))//"_"//lt_bath//"pdb"
+ write (iout,*) "pdb ",pdbfilename
+ call flush(iout)
+ open(ipdb,file=pdbfilename,position="append")
+c write (tytul,'("Conformation",i10," T=",f5.1)')
+c & kk(islice),rt_bath
+ call pdbout(kk(islice),1.0d0/(rt_bath*1.987D-3),
+ & efree+0.0d0,rpotE+0.0d0,efree+0.0d0,rmsdev+0.0d0)
+ close(ipdb)
+#ifdef MPI
+ endif
+#endif
+#endif
+#ifdef DEBUG
+ call int_from_cart1(.false.)
+ write (iout,*) "Writing conformation, record",ll(islice)
+ write (iout,*) "Cartesian coordinates"
+ write (iout,'(8f10.5)') ((c(j,i),j=1,3),i=1,nres)
+ write (iout,'(8f10.5)') ((c(j,i+nres),j=1,3),i=nnt,nct)
+ write (iout,*) "Internal coordinates"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+c write (iout,'(8f10.5)') (rprop(j),j=1,nQ)
+ write (iout,'(16i5)') iscor
+ call flush(iout)
+#endif
+ endif
+ endif
+
+ 112 continue
+
+ enddo
+ close(ientout)
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfclose_(ixdrf, iret)
+#else
+ call xdrfclose(ixdrf, iret)
+#endif
+ write (iout,'(i10," trajectories found in file.")') ntraj+1
+ write (iout,'(a)') "Numbers of steps in trajectories:"
+ write (iout,'(8i10)') (nstep(i),i=0,ntraj)
+ write (iout,*) ii," conformations read from file",
+ & nazwa(:ilen(nazwa))
+ do islice=1,nslice
+ write (iout,*) mm(islice)," conformations read so far, slice",
+ & islice
+ write (iout,*) ll(islice),
+ & " conformations stored so far, slice",islice
+ enddo
+ call flush(iout)
+ return
+ end
--- /dev/null
+ subroutine cxread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm,*)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ integer MaxTraj
+ parameter (MaxTraj=2050)
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.HEADER'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.PROTFILES'
+ include 'COMMON.OBCINKA'
+ include 'COMMON.FREE'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.PROT'
+ character*64 nazwa,bprotfile_temp
+ real*4 rtime,rpotE,ruconst,rt_bath,rprop(maxQ)
+ double precision time
+ integer iret,itmp,itraj,ntraj
+ real xoord(3,maxres2+2),prec
+ integer nstep(0:MaxTraj-1)
+ integer ilen
+ external ilen
+ integer ii,jj(maxslice),kk(maxslice),ll(maxslice),mm(maxslice)
+ integer is(MaxSlice),ie(MaxSlice),nrec_slice
+ double precision ts(MaxSlice),te(MaxSlice),time_slice
+ integer slice
+ call set_slices(is,ie,ts,te,iR,ib,iparm)
+
+ do i=1,nQ
+ rprop(i)=0.0d0
+ enddo
+ do i=0,MaxTraj-1
+ nstep(i)=0
+ enddo
+ ntraj=0
+ it=0
+ iret=1
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfopen_(ixdrf,nazwa, "r", iret)
+#else
+ call xdrfopen(ixdrf,nazwa, "r", iret)
+#endif
+ if (iret.eq.0) return1
+
+ islice1=1
+ call opentmp(islice1,ientout,bprotfile_temp)
+c print *,"bumbum"
+ do while (iret.gt.0)
+
+#if (defined(AIX) && !defined(JUBL))
+ call xdrffloat_(ixdrf, rtime, iret)
+c print *,"rtime",rtime," iret",iret
+ call xdrffloat_(ixdrf, rpotE, iret)
+c write (iout,*) "rpotE",rpotE," iret",iret
+ call flush(iout)
+ call xdrffloat_(ixdrf, ruconst, iret)
+ call xdrffloat_(ixdrf, rt_bath, iret)
+ call xdrfint_(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint_(ixdrf, ihpb(j), iret)
+ call xdrfint_(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrfint_(ixdrf, nprop, iret)
+ do i=1,nprop
+ call xdrffloat_(ixdrf, rprop(i), iret)
+ enddo
+#else
+ call xdrffloat(ixdrf, rtime, iret)
+ call xdrffloat(ixdrf, rpotE, iret)
+c write (iout,*) "rpotE",rpotE," iret",iret
+ call flush(iout)
+ call xdrffloat(ixdrf, ruconst, iret)
+ call xdrffloat(ixdrf, rt_bath, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrfint(ixdrf, nprop, iret)
+c write (iout,*) "nprop",nprop
+ call flush(iout)
+ do i=1,nprop
+ call xdrffloat(ixdrf, rprop(i), iret)
+ enddo
+#endif
+ if (iret.eq.0) exit
+ itraj=mod(it,totraj(iR,iparm))
+#ifdef DEBUG
+ write (iout,*) "ii",ii," itraj",itraj
+#endif
+ call flush(iout)
+ it=it+1
+ if (itraj.gt.ntraj) ntraj=itraj
+ nstep(itraj)=nstep(itraj)+1
+#ifdef DEBUG
+ write (iout,*) rtime,rpotE,rt_bath,nss,
+ & (ihpb(j),jhpb(j),j=1,nss),(rprop(j),j=1,nprop)
+ call flush(iout)
+#endif
+ prec=10000.0
+
+ itmp=0
+#if (defined(AIX) && !defined(JUBL))
+ call xdrf3dfcoord_(ixdrf, xoord, itmp, prec, iret)
+#else
+ call xdrf3dfcoord(ixdrf, xoord, itmp, prec, iret)
+#endif
+#ifdef DEBUG
+ write (iout,'(10f8.3)') ((xoord(j,i),j=1,3),i=1,itmp)
+#endif
+ if (iret.eq.0) exit
+ if (itmp .ne. nres + nct - nnt + 1) then
+ write (iout,*) "Error: inconsistent sizes",itmp,nres+nct-nnt+1
+ call flush(iout)
+ exit
+ endif
+
+ time=rtime
+c write (iout,*) "calling slice"
+c call flush(iout)
+ islice=slice(nstep(itraj),time,is,ie,ts,te)
+c write (iout,*) "islice",islice
+c call flush(iout)
+
+ if (islice.gt.0 .and. islice.le.nslice) then
+ ii=ii+1
+ kk(islice)=kk(islice)+1
+ mm(islice)=mm(islice)+1
+ if (mod(nstep(itraj),isampl(iparm)).eq.0) then
+ if (replica(iparm)) then
+ rt_bath=1.0d0/(rt_bath*1.987D-3)
+ do i=1,nT_h(iparm)
+ if (abs(real(beta_h(i,iparm))-rt_bath).lt.1.0e-4) then
+ iib = i
+ goto 22
+ endif
+ enddo
+ 22 continue
+ if (i.gt.nT_h(iparm)) then
+ write (iout,*) "Error - temperature of conformation",
+ & ii,1.0d0/(rt_bath*1.987D-3),
+ & " does not match any of the list"
+ write (iout,*)
+ & 1.0d0/(rt_bath*1.987D-3),
+ & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+ call flush(iout)
+ exit
+ call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
+ endif
+ else
+ iib = ib
+ endif
+
+ efree=0.0d0
+ jj(islice)=jj(islice)+1
+ snk(iR,iib,iparm,islice)=snk(iR,iib,iparm,islice)+1
+ ll(islice)=ll(islice)+1
+#ifdef DEBUG
+ write (iout,*) "Writing conformation, record",ll(islice)
+ write (iout,*) "ib",ib," iib",iib
+ write (iout,*) "ntraj",ntraj," itraj",itraj,
+ & " nstep",nstep(itraj)
+ write (iout,*) "pote",rpotE," time",rtime
+c if (replica(iparm)) then
+c write (iout,*) "TEMP",1.0d0/(rt_bath*1.987D-3)
+c write (iout,*) "TEMP list"
+c write (iout,*)
+c & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+c endif
+ write (iout,*) "iparm",iparm," ib",ib," iR",iR," nQ",nQ
+c write (iout,*) "nres",nres," nnt",nnt," nct",nct," nss",nss
+c write (iout,*) "length",nres*4+(nct-nnt+1)*4+4+2*nss*4
+ call flush(iout)
+#endif
+ if (islice.ne.islice1) then
+c write (iout,*) "islice",islice," islice1",islice1
+ close(ientout)
+c write (iout,*) "Closing file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+ call opentmp(islice,ientout,bprotfile_temp)
+c write (iout,*) "Opening file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+ islice1=islice
+ endif
+ write(ientout,rec=ll(islice))
+ & ((xoord(l,k),l=1,3),k=1,nres),
+ & ((xoord(l,k),l=1,3),k=nres+1,nres+nct-nnt+1),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & rpotE+0.0d0,efree,rmsdev,(rprop(i)+0.0d0,i=1,nQ),
+ & iR,iib,iparm
+#ifdef DEBUG
+ do i=1,nres
+ do j=1,3
+ c(j,i)=xoord(j,i)
+ enddo
+ enddo
+ do i=1,nct-nnt+1
+ do j=1,3
+ c(j,i+nres+nnt-1)=xoord(j,i+nres)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ write (iout,*) "Writing conformation, record",ll(islice)
+ write (iout,*) "Cartesian coordinates"
+ write (iout,'(8f10.5)') ((c(j,i),j=1,3),i=1,nres)
+ write (iout,'(8f10.5)') ((c(j,i+nres),j=1,3),i=nnt,nct)
+ write (iout,*) "Internal coordinates"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+c write (iout,'(8f10.5)') (rprop(j),j=1,nQ)
+ write (iout,'(16i5)') iscor
+ call flush(iout)
+#endif
+ endif
+ endif
+
+ enddo
+ 112 continue
+ close(ientout)
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfclose_(ixdrf, iret)
+#else
+ call xdrfclose(ixdrf, iret)
+#endif
+ write (iout,'(i10," trajectories found in file.")') ntraj+1
+ write (iout,'(a)') "Numbers of steps in trajectories:"
+ write (iout,'(8i10)') (nstep(i),i=0,ntraj)
+ write (iout,*) ii," conformations read from file",
+ & nazwa(:ilen(nazwa))
+ do islice=1,nslice
+ write (iout,*) mm(islice)," conformations read so far, slice",
+ & islice
+ write (iout,*) ll(islice),
+ & " conformations stored so far, slice",islice
+ enddo
+ call flush(iout)
+ return
+ end
--- /dev/null
+ subroutine define_pairs
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.COMPAR'
+ include 'COMMON.FRAG'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.GEO'
+ include 'COMMON.CONTACTS1'
+ include 'COMMON.PEPTCONT'
+ do j=1,nfrag(1)
+ length_frag = 0
+ do k=1,npiece(j,1)
+ length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
+ enddo
+ len_frag(j,1)=length_frag
+ write (iout,*) "Fragment",j," length",len_frag(j,1)
+ enddo
+ nfrag(2)=0
+ do i=1,nfrag(1)
+ do j=i+1,nfrag(1)
+ ind = icant(i,j)
+ if (istruct(i).le.1 .or. istruct(j).le.1) then
+ if (istruct(i).le.1) then
+ ll1=len_frag(i,1)
+ else
+ ll1=len_frag(i,1)/2
+ endif
+ if (istruct(j).le.1) then
+ ll2=len_frag(j,1)
+ else
+ ll2=len_frag(j,1)/2
+ endif
+ len_cut=max0(min0(ll1*2/3,ll2*4/5),3)
+ else
+ if (istruct(i).eq.2 .or. istruct(i).eq.4) then
+ ll1=len_frag(i,1)/2
+ else
+ ll1=len_frag(i,1)
+ endif
+ if (istruct(j).eq.2 .or. istruct(j).eq.4) then
+ ll2=len_frag(j,1)/2
+ else
+ ll2=len_frag(j,1)
+ endif
+ len_cut=max0(min0(ll1*4/5,ll2)*4/5,3)
+ endif
+ write (iout,*) "Fragments",i,j," structure",istruct(i),
+ & istruct(j)," # contacts",
+ & ncont_frag_ref(ind),nsccont_frag_ref(ind),
+ & " lengths",len_frag(i,1),len_frag(j,1),
+ & " ll1",ll1," ll2",ll2," len_cut",len_cut
+ if ((istruct(i).eq.1 .or. istruct(j).eq.1) .and.
+ & nsccont_frag_ref(ind).ge.len_cut ) then
+ if (istruct(i).eq.1 .and. istruct(j).eq.1) then
+ write (iout,*) "Adding pair of helices",i,j,
+ & " based on SC contacts"
+ else
+ write (iout,*) "Adding helix+strand/sheet pair",i,j,
+ & " based on SC contacts"
+ endif
+ nfrag(2)=nfrag(2)+1
+ if (icont_pair.gt.0) then
+ write (iout,*) "# SC contacts will be used",
+ & " in comparison."
+ isccont(nfrag(2),2)=1
+ endif
+ if (irms_pair.gt.0) then
+ write (iout,*) "Fragment RMSD will be used",
+ & " in comparison."
+ irms(nfrag(2),2)=1
+ endif
+ npiece(nfrag(2),2)=2
+ ipiece(1,nfrag(2),2)=i
+ ipiece(2,nfrag(2),2)=j
+ ielecont(nfrag(2),2)=0
+ n_shift(1,nfrag(2),2)=nshift_pair
+ n_shift(2,nfrag(2),2)=nshift_pair
+ nc_fragm(nfrag(2),2)=ncfrac_pair
+ nc_req_setf(nfrag(2),2)=ncreq_pair
+ else if ((istruct(i).ge.2 .and. istruct(i).le.4)
+ & .and. (istruct(j).ge.2 .and. istruct(i).le.4)
+ & .and. ncont_frag_ref(ind).ge.len_cut ) then
+ nfrag(2)=nfrag(2)+1
+ write (iout,*) "Adding pair strands/sheets",i,j,
+ & " based on pp contacts"
+ if (icont_pair.gt.0) then
+ write (iout,*) "# pp contacts will be used",
+ & " in comparison."
+ ielecont(nfrag(2),2)=1
+ endif
+ if (irms_pair.gt.0) then
+ write (iout,*) "Fragment RMSD will be used",
+ & " in comparison."
+ irms(nfrag(2),2)=1
+ endif
+ npiece(nfrag(2),2)=2
+ ipiece(1,nfrag(2),2)=i
+ ipiece(2,nfrag(2),2)=j
+ ielecont(nfrag(2),2)=1
+ isccont(nfrag(2),2)=0
+ n_shift(1,nfrag(2),2)=nshift_pair
+ n_shift(2,nfrag(2),2)=nshift_pair
+ nc_fragm(nfrag(2),2)=ncfrac_bet
+ nc_req_setf(nfrag(2),2)=ncreq_bet
+ endif
+ enddo
+ enddo
+ write (iout,*) "Pairs found"
+ do i=1,nfrag(2)
+ write (iout,*) ipiece(1,i,2),ipiece(2,i,2)
+ enddo
+ return
+ end
--- /dev/null
+ subroutine elecont(lprint,ncont,icont,ist,ien)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ include 'COMMON.LOCAL'
+ logical lprint
+ integer i,j,k,ist,ien,iteli,itelj,ind,i1,i2,it1,it2,ic1,ic2
+ double precision rri,xi,yi,zi,dxi,dyi,dzi,xmedi,ymedi,zmedi,
+ & xj,yj,zj,dxj,dyj,dzj,aaa,bbb,ael6i,ael3i,rrmij,rmij,r3ij,r6ij,
+ & vrmij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,evdwij,el1,el2,
+ & eesij,ees,evdw,ene
+ double precision elpp6c(2,2),elpp3c(2,2),ael6c(2,2),ael3c(2,2),
+ & appc(2,2),bppc(2,2)
+ double precision elcutoff,elecutoff_14
+ integer ncont,icont(2,maxcont)
+ double precision econt(maxcont)
+*
+* Load the constants of peptide bond - peptide bond interactions.
+* Type 1 - ordinary peptide bond, type 2 - alkylated peptide bond (e.g.
+* proline) - determined by averaging ECEPP energy.
+*
+* as of 7/06/91.
+*
+c data epp / 0.3045d0, 0.3649d0, 0.3649d0, 0.5743d0/
+c data rpp / 4.5088d0, 4.5395d0, 4.5395d0, 4.4846d0/
+ data elpp6c /-0.2379d0,-0.2056d0,-0.2056d0,-0.0610d0/
+ data elpp3c / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
+ data elcutoff /-0.3d0/,elecutoff_14 /-0.5d0/
+ ees=0.0d0
+ evdw=0.0d0
+ if (lprint) write (iout,'(a)')
+ & "Constants of electrostatic interaction energy expression."
+ do i=1,2
+ do j=1,2
+ rri=rpp(i,j)**6
+ appc(i,j)=epp(i,j)*rri*rri
+ bppc(i,j)=-2.0*epp(i,j)*rri
+ ael6c(i,j)=elpp6c(i,j)*4.2**6
+ ael3c(i,j)=elpp3c(i,j)*4.2**3
+ if (lprint)
+ & write (iout,'(2i2,4e15.4)') i,j,appc(i,j),bppc(i,j),ael6c(i,j),
+ & ael3c(i,j)
+ enddo
+ enddo
+ ncont=0
+ do 1 i=ist,ien-2
+ xi=c(1,i)
+ yi=c(2,i)
+ zi=c(3,i)
+ dxi=c(1,i+1)-c(1,i)
+ dyi=c(2,i+1)-c(2,i)
+ dzi=c(3,i+1)-c(3,i)
+ xmedi=xi+0.5*dxi
+ ymedi=yi+0.5*dyi
+ zmedi=zi+0.5*dzi
+ do 4 j=i+2,ien-1
+ ind=ind+1
+ iteli=itel(i)
+ itelj=itel(j)
+ if (j.eq.i+2 .and. itelj.eq.2) iteli=2
+ if (iteli.eq.2 .and. itelj.eq.2) goto 4
+ aaa=appc(iteli,itelj)
+ bbb=bppc(iteli,itelj)
+ ael6i=ael6c(iteli,itelj)
+ ael3i=ael3c(iteli,itelj)
+ dxj=c(1,j+1)-c(1,j)
+ dyj=c(2,j+1)-c(2,j)
+ dzj=c(3,j+1)-c(3,j)
+ xj=c(1,j)+0.5*dxj-xmedi
+ yj=c(2,j)+0.5*dyj-ymedi
+ zj=c(3,j)+0.5*dzj-zmedi
+ rrmij=1.0/(xj*xj+yj*yj+zj*zj)
+ rmij=sqrt(rrmij)
+ r3ij=rrmij*rmij
+ r6ij=r3ij*r3ij
+ vrmij=vblinv*rmij
+ cosa=(dxi*dxj+dyi*dyj+dzi*dzj)*vblinv2
+ cosb=(xj*dxi+yj*dyi+zj*dzi)*vrmij
+ cosg=(xj*dxj+yj*dyj+zj*dzj)*vrmij
+ fac=cosa-3.0*cosb*cosg
+ ev1=aaa*r6ij*r6ij
+ ev2=bbb*r6ij
+ fac3=ael6i*r6ij
+ fac4=ael3i*r3ij
+ evdwij=ev1+ev2
+ el1=fac3*(4.0+fac*fac-3.0*(cosb*cosb+cosg*cosg))
+ el2=fac4*fac
+ eesij=el1+el2
+ if (j.gt.i+2 .and. eesij.le.elcutoff .or.
+ & j.eq.i+2 .and. eesij.le.elecutoff_14) then
+ ncont=ncont+1
+ icont(1,ncont)=i
+ icont(2,ncont)=j
+ econt(ncont)=eesij
+ endif
+ ees=ees+eesij
+ evdw=evdw+evdwij
+ 4 continue
+ 1 continue
+ if (lprint) then
+ write (iout,*) 'Total average electrostatic energy: ',ees
+ write (iout,*) 'VDW energy between peptide-group centers: ',evdw
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts before pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
+ & i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+c For given residues keep only the contacts with the greatest energy.
+ i=0
+ do while (i.lt.ncont)
+ i=i+1
+ ene=econt(i)
+ ic1=icont(1,i)
+ ic2=icont(2,i)
+ j=i
+ do while (j.lt.ncont)
+ j=j+1
+ if (ic1.eq.icont(1,j).and.iabs(icont(2,j)-ic2).le.2 .or.
+ & ic2.eq.icont(2,j).and.iabs(icont(1,j)-ic1).le.2) then
+c write (iout,*) "i",i," j",j," ic1",ic1," ic2",ic2,
+c & " jc1",icont(1,j)," jc2",icont(2,j)," ncont",ncont
+ if (econt(j).lt.ene .and. icont(2,j).ne.icont(1,j)+2) then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.icont(2,j)
+ & .and. iabs(icont(1,k)-ic1).le.2 .and.
+ & econt(k).lt.econt(j) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.icont(1,j)
+ & .and. iabs(icont(2,k)-ic2).le.2 .and.
+ & econt(k).lt.econt(j) ) goto 21
+ enddo
+ endif
+c Remove ith contact
+ do k=i+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ i=i-1
+ ncont=ncont-1
+c write (iout,*) "ncont",ncont
+c do k=1,ncont
+c write (iout,*) icont(1,k),icont(2,k)
+c enddo
+ goto 20
+ else if (econt(j).gt.ene .and. ic2.ne.ic1+2)
+ & then
+ if (ic1.eq.icont(1,j)) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(2,k).eq.ic2
+ & .and. iabs(icont(1,k)-icont(1,j)).le.2 .and.
+ & econt(k).lt.econt(i) ) goto 21
+ enddo
+ else if (ic2.eq.icont(2,j) ) then
+ do k=1,ncont
+ if (k.ne.i .and. k.ne.j .and. icont(1,k).eq.ic1
+ & .and. iabs(icont(2,k)-icont(2,j)).le.2 .and.
+ & econt(k).lt.econt(i) ) goto 21
+ enddo
+ endif
+c Remove jth contact
+ do k=j+1,ncont
+ icont(1,k-1)=icont(1,k)
+ icont(2,k-1)=icont(2,k)
+ econt(k-1)=econt(k)
+ enddo
+ ncont=ncont-1
+c write (iout,*) "ncont",ncont
+c do k=1,ncont
+c write (iout,*) icont(1,k),icont(2,k)
+c enddo
+ j=j-1
+ endif
+ endif
+ 21 continue
+ enddo
+ 20 continue
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) 'Electrostatic contacts after pruning: '
+ do i=1,ncont
+ i1=icont(1,i)
+ i2=icont(2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,f10.5)')
+ & i,restyp(it1),i1,restyp(it2),i2,econt(i)
+ enddo
+ endif
+ return
+ end
--- /dev/null
+ subroutine enecalc(islice,*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.SBRIDGE"
+ include "COMMON.GEO"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.LOCAL"
+ include "COMMON.WEIGHTS"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.CONTROL"
+ include "COMMON.TORCNSTR"
+ character*64 nazwa
+ character*80 bxname
+ character*3 liczba
+ double precision qwolynes
+ external qwolynes
+ integer errmsg_count,maxerrmsg_count /100/
+ double precision rmsnat,gyrate
+ external rmsnat,gyrate
+ double precision tole /1.0d-1/
+ integer i,itj,ii,iii,j,k,l,licz
+ integer ir,ib,ipar,iparm
+ integer iscor,islice
+ real*4 csingle(3,maxres2)
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ double precision energia(0:max_ene),rmsdev,efree,eini
+ double precision fT(6),quot,quotl,kfacl,kfac /2.4d0/,T0 /3.0d2/
+ double precision tt
+ integer snk_p(MaxR,MaxT_h,Max_parm)
+ logical lerr
+ character*64 bprotfile_temp
+ call opentmp(islice,ientout,bprotfile_temp)
+ iii=0
+ ii=0
+ errmsg_count=0
+ write (iout,*) "enecalc: nparmset ",nparmset
+#ifdef MPI
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ snk_p(i,ib,iparm)=0
+ enddo
+ enddo
+ enddo
+ do i=indstart(me1),indend(me1)
+#else
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ snk(i,ib,iparm)=0
+ enddo
+ enddo
+ enddo
+ do i=1,ntot
+#endif
+ read(ientout,rec=i,err=101)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,(q(j,iii+1),j=1,nQ),iR,ib,ipar
+ if (indpdb.gt.0) then
+ do k=1,nres
+ do l=1,3
+ c(l,k)=csingle(l,k)
+ enddo
+ enddo
+ do k=nnt,nct
+ do l=1,3
+ c(l,k+nres)=csingle(l,k+nres)
+ enddo
+ enddo
+ q(nQ+1,iii+1)=rmsnat(iii+1)
+ endif
+ q(nQ+2,iii+1)=gyrate(iii+1)
+c fT=T0*beta_h(ib,ipar)*1.987D-3
+c ft=2.0d0/(1.0d0+1.0d0/(T0*beta_h(ib,ipar)*1.987D-3))
+ if (rescale_mode.eq.1) then
+ quot=1.0d0/(T0*beta_h(ib,ipar)*1.987D-3)
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,ipar)*1.987D-3)
+ ft(6)=(320.0+80.0*dtanh((tt-320.0)/80.0))/320.0
+#elif defined(FUNCT)
+ ft(6)=quot
+#else
+ ft(6)=1.0d0
+#endif
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ fT(l)=kfacl/(kfacl-1.0d0+quotl)
+ enddo
+ else if (rescale_mode.eq.2) then
+ quot=1.0d0/(T0*beta_h(ib,ipar)*1.987D-3)
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,ipar)*1.987D-3)
+ ft(6)=(320.0+80.0*dtanh((tt-320.0)/80.0))/320.0
+#elif defined(FUNCT)
+ ft(6)=quot
+#else
+ ft(6)=1.0d0
+#endif
+ quotl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ fT(l)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+ else if (rescale_mode.eq.0) then
+ do l=1,5
+ fT(l)=1.0d0
+ enddo
+ else
+ write (iout,*) "Error in ECECALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+
+c write (iout,*) "T",1.0d0/(beta_h(ib,ipar)*1.987D-3)," T0",T0,
+c & " kfac",kfac,"quot",quot," fT",fT
+ do j=1,2*nres
+ do k=1,3
+ c(k,j)=csingle(k,j)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ ii=ii+1
+ do iparm=1,nparmset
+
+ call restore_parm(iparm)
+#ifdef DEBUG
+ write (iout,*) wsc,wscp,welec,wvdwpp,wang,wtor,wscloc,
+ & wcorr,wcorr5,wcorr6,wturn4,wturn3,wturn6,wel_loc,
+ & wtor_d,wsccor,wbond
+#endif
+c write (iout,*) "Calling ETOTAL"
+ call etotal(energia(0),fT,beta_h(ib,iparm))
+#ifdef DEBUG
+ write (iout,*) "Conformation",i
+ call enerprint(energia(0),fT)
+c write (iout,'(2i5,21f8.2)') i,iparm,(energia(k),k=1,21)
+c write (iout,*) "ftors",ftors
+c call intout
+#endif
+ if (energia(0).ge.1.0d20) then
+ write (iout,*) "NaNs detected in some of the energy",
+ & " components for conformation",ii+1
+ write (iout,*) "The Cartesian geometry is:"
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,*) "The internal geometry is:"
+c call intout
+c call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,*) "The components of the energy are:"
+ call enerprint(energia(0),fT)
+ write (iout,*)
+ & "This conformation WILL NOT be added to the database."
+ call flush(iout)
+ goto 121
+ else
+#ifdef DEBUG
+ if (ipar.eq.iparm) write (iout,*) i,iparm,
+ & 1.0d0/(beta_h(ib,ipar)*1.987D-3),eini,energia(0)
+#endif
+ if (ipar.eq.iparm .and. einicheck.gt.0 .and.
+ & dabs(eini-energia(0)).gt.tole) then
+ if (errmsg_count.le.maxerrmsg_count) then
+ write (iout,'(2a,2e15.5,a,2i8,a,f8.1)')
+ & "Warning: energy differs remarkably from ",
+ & " the value read in: ",energia(0),eini," point",
+ & iii+1,indstart(me1)+iii," T",
+ & 1.0d0/(1.987D-3*beta_h(ib,ipar))
+ errmsg_count=errmsg_count+1
+ if (errmsg_count.gt.maxerrmsg_count)
+ & write (iout,*) "Too many warning messages"
+ if (einicheck.gt.1) then
+ write (iout,*) "Calculation stopped."
+ call flush(iout)
+#ifdef MPI
+ call MPI_Abort(WHAM_COMM,IERROR,ERRCODE)
+#endif
+ call flush(iout)
+ return1
+ endif
+ endif
+ endif
+ potE(iii+1,iparm)=energia(0)
+ do k=1,21
+ enetb(k,iii+1,iparm)=energia(k)
+ enddo
+#ifdef DEBUG
+ write (iout,'(2i5,f10.1,3e15.5)') i,iii,
+ & 1.0d0/(beta_h(ib,ipar)*1.987D-3),energia(0),eini,efree
+ call enerprint(energia(0),fT)
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+ write (iout,'(8f10.5)') (q(k,iii+1),k=1,nQ)
+ write (iout,'(f10.5,i10)') rmsdev,iscor
+ call enerprint(energia(0),fT)
+ write(liczba,'(bz,i3.3)') me
+ nazwa="test"//liczba//".pdb"
+ write (iout,*) "pdb file",nazwa
+ open (ipdb,file=nazwa,position="append")
+ call pdbout(ii+1,beta_h(ib,ipar),efree,energia(0),0.0d0,rmsdev)
+ close(ipdb)
+#endif
+ endif
+
+ enddo ! iparm
+
+ iii=iii+1
+ if (q(1,iii).le.0.0d0 .and. indpdb.gt.0) q(1,iii)=qwolynes(0,0)
+ write (ientout,rec=iii)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & potE(iii,ipar),efree,rmsdev,(q(k,iii),k=1,nQ),iR,ib,ipar
+c write (iout,'(2i5,2e15.5)') ii,iii,potE(iii,ipar),efree
+#ifdef MPI
+ if (separate_parset) then
+ snk_p(iR,ib,1)=snk_p(iR,ib,1)+1
+ else
+ snk_p(iR,ib,ipar)=snk_p(iR,ib,ipar)+1
+ endif
+c write (iout,*) "iii",iii," iR",iR," ib",ib," ipar",ipar,
+c & " snk",snk_p(iR,ib,ipar)
+#else
+ snk(iR,ib,ipar,islice)=snk(iR,ib,ipar,islice)+1
+#endif
+ 121 continue
+ enddo
+#ifdef MPI
+ scount(me)=iii
+ write (iout,*) "Me",me," scount",scount(me)
+ call flush(iout)
+c Master gathers updated numbers of conformations written by all procs.
+ call MPI_AllGather( scount(me), 1, MPI_INTEGER, scount(0), 1,
+ & MPI_INTEGER, WHAM_COMM, IERROR)
+ indstart(0)=1
+ indend(0)=scount(0)
+ do i=1, Nprocs-1
+ indstart(i)=indend(i-1)+1
+ indend(i)=indstart(i)+scount(i)-1
+ enddo
+ write (iout,*)
+ write (iout,*) "Revised conformation counts"
+ do i=0,nprocs1-1
+ write (iout,'(a,i5,a,i7,a,i7,a,i7)')
+ & "Processor",i," indstart",indstart(i),
+ & " indend",indend(i)," count",scount(i)
+ enddo
+ call flush(iout)
+ call MPI_AllReduce(snk_p(1,1,1),snk(1,1,1,islice),
+ & MaxR*MaxT_h*nParmSet,
+ & MPI_INTEGER,MPI_SUM,WHAM_COMM,IERROR)
+#endif
+ stot(islice)=0
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ stot(islice)=stot(islice)+snk(i,ib,iparm,islice)
+ enddo
+ enddo
+ enddo
+ write (iout,*) "Revised SNK"
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ write (iout,'("Param",i3," Temp",f6.1,3x,32i8)')
+ & iparm,1.0d0/(1.987D-3*beta_h(ib,iparm)),
+ & (snk(i,ib,iparm,islice),i=1,nR(ib,iparm))
+ write (iout,*) "snk_p",(snk_p(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+ write (iout,'("Total",i10)') stot(islice)
+ call flush(iout)
+ return
+ 101 write (iout,*) "Error in scratchfile."
+ call flush(iout)
+ return1
+ end
+c------------------------------------------------------------------------------
+ subroutine write_dbase(islice,*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "DIMENSIONS.COMPAR"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CONTROL"
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.SBRIDGE"
+ include "COMMON.GEO"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.LOCAL"
+ include "COMMON.WEIGHTS"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.COMPAR"
+ include "COMMON.PROT"
+ character*64 nazwa
+ character*80 bxname,cxname
+ character*64 bprotfile_temp
+ character*3 liczba,licz
+ character*2 licz2
+ integer i,itj,ii,iii,j,k,l
+ integer ixdrf,iret
+ integer iscor,islice
+ double precision rmsdev,efree,eini
+ real*4 csingle(3,maxres2)
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ integer ir,ib,iparm
+ write (licz2,'(bz,i2.2)') islice
+ call opentmp(islice,ientout,bprotfile_temp)
+ write (iout,*) "bprotfile_temp ",bprotfile_temp
+ call flush(iout)
+ if (.not.bxfile .and. .not. cxfile .and. indpdb.eq.0
+ & .and. ensembles.eq.0) then
+ close(ientout,status="delete")
+ return
+ endif
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ if (bxfile .or. cxfile .or. ensembles.gt.0) then
+ if (.not.separate_parset) then
+ bxname = prefix(:ilen(prefix))//liczba//".bx"
+ else
+ write (licz,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//liczba//"_par"//licz//".bx"
+ endif
+ open (ientin,file=bxname,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec1)
+ endif
+#else
+ if (bxfile .or. cxfile .or. ensembles.gt.0) then
+ if (nslice.eq.1) then
+ bxname = prefix(:ilen(prefix))//".bx"
+ else
+ bxname = prefix(:ilen(prefix))//
+ & "_slice_"//licz2//".bx"
+ endif
+ open (ientin,file=bxname,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec1)
+ write (iout,*) "Calculating energies; writing geometry",
+ & " and energy components to ",bxname(:ilen(bxname))
+ endif
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfopen_(ixdrf,cxname, "w", iret)
+#else
+ call xdrfopen(ixdrf,cxname, "w", iret)
+#endif
+ if (iret.eq.0) then
+ write (iout,*) "Error opening cxfile ",cxname(:ilen(cxname))
+ cxfile=.fale.
+ endif
+ endif
+#endif
+ if (indpdb.gt.0) then
+ if (nslice.eq.1) then
+#ifdef MPI
+ if (.not.separate_parset) then
+ statname=prefix(:ilen(prefix))//'_'//pot(:ilen(pot))
+ & //liczba//'.stat'
+ else
+ write (licz,'(bz,i3.3)') myparm
+ statname=prefix(:ilen(prefix))//'_par'//licz//'_'//
+ & pot(:ilen(pot))//liczba//'.stat'
+ endif
+
+#else
+ statname=prefix(:ilen(prefix))//'_'//pot(:ilen(pot))//'.stat'
+#endif
+ else
+#ifdef MPI
+ if (.not.separate_parset) then
+ statname=prefix(:ilen(prefix))//'_'//pot(:ilen(pot))//
+ & "_slice_"//licz2//liczba//'.stat'
+ else
+ write (licz,'(bz,i3.3)') myparm
+ statname=prefix(:ilen(prefix))//'_'//pot(:ilen(pot))//
+ & '_par'//licz//"_slice_"//licz2//liczba//'.stat'
+ endif
+#else
+ statname=prefix(:ilen(prefix))//'_'//pot(:ilen(pot))
+ & //"_slice_"//licz2//'.stat'
+#endif
+ endif
+ open(istat,file=statname,status="unknown")
+ endif
+
+#ifdef MPI
+ do i=1,scount(me)
+#else
+ do i=1,ntot(islice)
+#endif
+ read(ientout,rec=i,err=101)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,(q(k,i),k=1,nQ),iR,ib,iparm
+c write (iout,*) iR,ib,iparm,eini,efree
+ do j=1,2*nres
+ do k=1,3
+ c(k,j)=csingle(k,j)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ iscore=0
+ if (indpdb.gt.0) then
+ call conf_compar(i,.false.,.true.)
+ endif
+ if (bxfile .or.cxfile .or. ensembles.gt.0) write (ientin,rec=i)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+c & potE(i,iparm),-entfac(i),rms_nat,iscore
+ & potE(i,nparmset),-entfac(i),rms_nat,iscore
+c write (iout,'(2i5,3e15.5)') i,me,potE(i,iparm),-entfac(i)
+#ifndef MPI
+ if (cxfile) call cxwrite(ixdrf,csingle,potE(i,nparmset),
+ & -entfac(i),rms_nat,iscore)
+#endif
+ enddo
+ close(ientout,status="delete")
+ close(istat)
+ if (bxfile .or. cxfile .or. ensembles.gt.0) close(ientin)
+#ifdef MPI
+ call MPI_Barrier(WHAM_COMM,IERROR)
+ if (me.ne.Master .or. .not.bxfile .and. .not. cxfile
+ & .and. ensembles.eq.0) return
+ write (iout,*)
+ if (bxfile .or. ensembles.gt.0) then
+ if (nslice.eq.1) then
+ if (.not.separate_parset) then
+ bxname = prefix(:ilen(prefix))//".bx"
+ else
+ write (licz,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//"_par"//licz//".bx"
+ endif
+ else
+ if (.not.separate_parset) then
+ bxname = prefix(:ilen(prefix))//"_slice_"//licz2//".bx"
+ else
+ write (licz,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//"par_"//licz//
+ & "_slice_"//licz2//".bx"
+ endif
+ endif
+ open (ientout,file=bxname,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec1)
+ write (iout,*) "Master is creating binary database ",
+ & bxname(:ilen(bxname))
+ endif
+ if (cxfile) then
+ if (nslice.eq.1) then
+ if (.not.separate_parset) then
+ cxname = prefix(:ilen(prefix))//".cx"
+ else
+ cxname = prefix(:ilen(prefix))//"_par"//licz//".cx"
+ endif
+ else
+ if (.not.separate_parset) then
+ cxname = prefix(:ilen(prefix))//
+ & "_slice_"//licz2//".cx"
+ else
+ cxname = prefix(:ilen(prefix))//"_par"//licz//
+ & "_slice_"//licz2//".cx"
+ endif
+ endif
+#if (defined(AIX) && !defined(JUBL))
+ call xdrfopen_(ixdrf,cxname, "w", iret)
+#else
+ call xdrfopen(ixdrf,cxname, "w", iret)
+#endif
+ if (iret.eq.0) then
+ write (iout,*) "Error opening cxfile ",cxname(:ilen(cxname))
+ cxfile=.false.
+ endif
+ endif
+ do j=0,nprocs-1
+ write (liczba,'(bz,i3.3)') j
+ if (separate_parset) then
+ write (licz,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//liczba//"_par"//licz//".bx"
+ else
+ bxname = prefix(:ilen(prefix))//liczba//".bx"
+ endif
+ open (ientin,file=bxname,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec1)
+ write (iout,*) "Master is reading conformations from ",
+ & bxname(:ilen(bxname))
+ iii = 0
+c write (iout,*) "j",j," indstart",indstart(j)," indend",indend(j)
+c call flush(iout)
+ do i=indstart(j),indend(j)
+ iii = iii+1
+ read(ientin,rec=iii,err=101)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,iscor
+ if (bxfile .or. ensembles.gt.0) then
+ write (ientout,rec=i)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,iscor
+ endif
+ if(cxfile)call cxwrite(ixdrf,csingle,eini,efree,rmsdev,iscor)
+#ifdef DEBUG
+ do k=1,2*nres
+ do l=1,3
+ c(l,k)=csingle(l,k)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ write (iout,'(2i5,3e15.5)') i,iii,eini,efree
+ write (iout,*) "The Cartesian geometry is:"
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,*) "The internal geometry is:"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+ write (iout,'(f10.5,i5)') rmsdev,iscor
+#endif
+ enddo ! i
+ write (iout,*) iii," conformations (from",indstart(j)," to",
+ & indend(j),") read from ",
+ & bxname(:ilen(bxname))
+ close (ientin,status="delete")
+ enddo ! j
+ if (bxfile .or. cxfile .or. ensembles.gt.0) close (ientout)
+#if (defined(AIX) && !defined(JUBL))
+ if (cxfile) call xdrfclose_(ixdrf,cxname,iret)
+#else
+ if (cxfile) call xdrfclose(ixdrf,cxname,iret)
+#endif
+#endif
+ return
+ 101 write (iout,*) "Error in scratchfile."
+ call flush(iout)
+ return1
+ end
+c-------------------------------------------------------------------------------
+ subroutine cxwrite(ixdrf,csingle,eini,efree,rmsdev,iscor)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "DIMENSIONS.COMPAR"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CONTROL"
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.SBRIDGE"
+ include "COMMON.GEO"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.LOCAL"
+ include "COMMON.WEIGHTS"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.COMPAR"
+ include "COMMON.PROT"
+ integer i,j,itmp,iscor,iret,ixdrf
+ double precision rmsdev,efree,eini
+ real*4 csingle(3,maxres2),xoord(3,maxres2+2)
+ real*4 prec
+
+c write (iout,*) "cxwrite"
+c call flush(iout)
+ prec=10000.0
+ do i=1,nres
+ do j=1,3
+ xoord(j,i)=csingle(j,i)
+ enddo
+ enddo
+ do i=nnt,nct
+ do j=1,3
+ xoord(j,nres+i-nnt+1)=csingle(j,i+nres)
+ enddo
+ enddo
+
+ itmp=nres+nct-nnt+1
+
+c write (iout,*) "itmp",itmp
+c call flush(iout)
+#if (defined(AIX) && !defined(JUBL))
+ call xdrf3dfcoord_(ixdrf, xoord, itmp, prec, iret)
+
+c write (iout,*) "xdrf3dfcoord"
+c call flush(iout)
+ call xdrfint_(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint_(ixdrf, ihpb(j), iret)
+ call xdrfint_(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat_(ixdrf,real(eini),iret)
+ call xdrffloat_(ixdrf,real(efree),iret)
+ call xdrffloat_(ixdrf,real(rmsdev),iret)
+ call xdrfint_(ixdrf,iscor,iret)
+#else
+ call xdrf3dfcoord(ixdrf, xoord, itmp, prec, iret)
+
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf,real(eini),iret)
+ call xdrffloat(ixdrf,real(efree),iret)
+ call xdrffloat(ixdrf,real(rmsdev),iret)
+ call xdrfint(ixdrf,iscor,iret)
+#endif
+
+ return
+ end
+c------------------------------------------------------------------------------
+ logical function conf_check(ii,iprint)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.SBRIDGE"
+ include "COMMON.GEO"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.LOCAL"
+ include "COMMON.WEIGHTS"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.CONTROL"
+ include "COMMON.TORCNSTR"
+ integer j,k,l,ii,itj,iprint
+ if (.not.check_conf) then
+ conf_check=.true.
+ return
+ endif
+ call int_from_cart1(.false.)
+ do j=nnt+1,nct
+ if (vbld(j).lt.2.0d0 .or. vbld(j).gt.5.0d0) then
+ if (iprint.gt.0)
+ & write (iout,*) "Bad CA-CA bond length",j," ",vbld(j),
+ & " for conformation",ii
+ if (iprint.gt.1) then
+ write (iout,*) "The Cartesian geometry is:"
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,*) "The internal geometry is:"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ endif
+ if (iprint.gt.0) write (iout,*)
+ & "This conformation WILL NOT be added to the database."
+ conf_check=.false.
+ return
+ endif
+ enddo
+ do j=nnt,nct
+ itj=itype(j)
+ if (itype(j).ne.10 .and. (vbld(nres+j)-dsc(itj)).gt.2.0d0) then
+ if (iprint.gt.0)
+ & write (iout,*) "Bad CA-SC bond length",j," ",vbld(nres+j),
+ & " for conformation",ii
+ if (iprint.gt.1) then
+ write (iout,*) "The Cartesian geometry is:"
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,*) "The internal geometry is:"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ endif
+ if (iprint.gt.0) write (iout,*)
+ & "This conformation WILL NOT be added to the database."
+ conf_check=.false.
+ return
+ endif
+ enddo
+ do j=3,nres
+ if (theta(j).le.0.0d0) then
+ if (iprint.gt.0)
+ & write (iout,*) "Zero theta angle(s) in conformation",ii
+ if (iprint.gt.1) then
+ write (iout,*) "The Cartesian geometry is:"
+ write (iout,'(8f10.5)') ((c(l,k),l=1,3),k=1,nres)
+ write (iout,'(8f10.5)') ((c(l,k+nres),l=1,3),k=nnt,nct)
+ write (iout,*) "The internal geometry is:"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ endif
+ if (iprint.gt.0) write (iout,*)
+ & "This conformation WILL NOT be added to the database."
+ conf_check=.false.
+ return
+ endif
+ if (theta(j).gt.179.97*deg2rad) theta(j)=179.97*deg2rad
+ enddo
+ conf_check=.true.
+c write (iout,*) "conf_check passed",ii
+ return
+ end
--- /dev/null
+ subroutine etotal(energia,fact)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+
+#ifndef ISNAN
+ external proc_proc
+#endif
+#ifdef WINPGI
+cMS$ATTRIBUTES C :: proc_proc
+#endif
+
+ include 'COMMON.IOUNITS'
+ double precision energia(0:max_ene),energia1(0:max_ene+1)
+#ifdef MPL
+ include 'COMMON.INFO'
+ external d_vadd
+ integer ready
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ double precision fact(6)
+cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot
+cd print *,'nnt=',nnt,' nct=',nct
+C
+C Compute the side-chain and electrostatic interaction energy
+C
+ goto (101,102,103,104,105,106) ipot
+C Lennard-Jones potential.
+ 101 call elj(evdw,evdw_t)
+cd print '(a)','Exit ELJ'
+ goto 107
+C Lennard-Jones-Kihara potential (shifted).
+ 102 call eljk(evdw,evdw_t)
+ goto 107
+C Berne-Pechukas potential (dilated LJ, angular dependence).
+ 103 call ebp(evdw,evdw_t)
+ goto 107
+C Gay-Berne potential (shifted LJ, angular dependence).
+ 104 call egb(evdw,evdw_t)
+ goto 107
+C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
+ 105 call egbv(evdw,evdw_t)
+ goto 107
+C New SC-SC potential
+ 106 call emomo(evdw,evdw_p,evdw_m)
+C
+C Calculate electrostatic (H-bonding) energy of the main chain.
+C
+ 107 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
+C
+C Calculate excluded-volume interaction energy between peptide groups
+C and side chains.
+C
+ call escp(evdw2,evdw2_14)
+c
+c Calculate the bond-stretching energy
+c
+ call ebond(estr)
+c write (iout,*) "estr",estr
+C
+C Calculate the disulfide-bridge and other energy and the contributions
+C from other distance constraints.
+cd print *,'Calling EHPB'
+ call edis(ehpb)
+cd print *,'EHPB exitted succesfully.'
+C
+C Calculate the virtual-bond-angle energy.
+C
+ call ebend(ebe)
+cd print *,'Bend energy finished.'
+C
+C Calculate the SC local energy.
+C
+ call esc(escloc)
+cd print *,'SCLOC energy finished.'
+C
+C Calculate the virtual-bond torsional energy.
+C
+cd print *,'nterm=',nterm
+ call etor(etors,edihcnstr,fact(1))
+C
+C 6/23/01 Calculate double-torsional energy
+C
+ call etor_d(etors_d,fact(2))
+C
+C 21/5/07 Calculate local sicdechain correlation energy
+C
+ call eback_sc_corr(esccor)
+C
+C 12/1/95 Multi-body terms
+C
+ n_corr=0
+ n_corr1=0
+ if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0
+ & .or. wturn6.gt.0.0d0) then
+c print *,"calling multibody_eello"
+ call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
+c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
+c print *,ecorr,ecorr5,ecorr6,eturn6
+ endif
+ if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then
+ call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
+ endif
+c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
+#ifdef SPLITELE
+ etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
+ & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
+ & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
+ & +wbond*estr+wsccor*fact(1)*esccor
+#else
+ etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
+ & +welec*fact(1)*(ees+evdw1)
+ & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
+ & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
+ & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
+ & +wbond*estr+wsccor*fact(1)*esccor
+#endif
+ energia(0)=etot
+ energia(1)=evdw
+#ifdef SCP14
+ energia(2)=evdw2-evdw2_14
+ energia(17)=evdw2_14
+#else
+ energia(2)=evdw2
+ energia(17)=0.0d0
+#endif
+#ifdef SPLITELE
+ energia(3)=ees
+ energia(16)=evdw1
+#else
+ energia(3)=ees+evdw1
+ energia(16)=0.0d0
+#endif
+ energia(4)=ecorr
+ energia(5)=ecorr5
+ energia(6)=ecorr6
+ energia(7)=eel_loc
+ energia(8)=eello_turn3
+ energia(9)=eello_turn4
+ energia(10)=eturn6
+ energia(11)=ebe
+ energia(12)=escloc
+ energia(13)=etors
+ energia(14)=etors_d
+ energia(15)=ehpb
+ energia(18)=estr
+ energia(19)=esccor
+ energia(20)=edihcnstr
+ energia(21)=evdw_t
+c detecting NaNQ
+#ifdef ISNAN
+#ifdef AIX
+ if (isnan(etot).ne.0) energia(0)=1.0d+99
+#else
+ if (isnan(etot)) energia(0)=1.0d+99
+#endif
+#else
+ i=0
+#ifdef WINPGI
+ idumm=proc_proc(etot,i)
+#else
+ call proc_proc(etot,i)
+#endif
+ if(i.eq.1)energia(0)=1.0d+99
+#endif
+#ifdef MPL
+c endif
+#endif
+ if (calc_grad) then
+C
+C Sum up the components of the Cartesian gradient.
+C
+#ifdef SPLITELE
+ do i=1,nct
+ do j=1,3
+ gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
+ & welec*fact(1)*gelc(j,i)+wvdwpp*gvdwpp(j,i)+
+ & wbond*gradb(j,i)+
+ & wstrain*ghpbc(j,i)+
+ & wcorr*fact(3)*gradcorr(j,i)+
+ & wel_loc*fact(2)*gel_loc(j,i)+
+ & wturn3*fact(2)*gcorr3_turn(j,i)+
+ & wturn4*fact(3)*gcorr4_turn(j,i)+
+ & wcorr5*fact(4)*gradcorr5(j,i)+
+ & wcorr6*fact(5)*gradcorr6(j,i)+
+ & wturn6*fact(5)*gcorr6_turn(j,i)+
+ & wsccor*fact(2)*gsccorc(j,i)
+ gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
+ & wbond*gradbx(j,i)+
+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
+ & wsccor*fact(2)*gsccorx(j,i)
+ enddo
+#else
+ do i=1,nct
+ do j=1,3
+ gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
+ & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+
+ & wbond*gradb(j,i)+
+ & wcorr*fact(3)*gradcorr(j,i)+
+ & wel_loc*fact(2)*gel_loc(j,i)+
+ & wturn3*fact(2)*gcorr3_turn(j,i)+
+ & wturn4*fact(3)*gcorr4_turn(j,i)+
+ & wcorr5*fact(4)*gradcorr5(j,i)+
+ & wcorr6*fact(5)*gradcorr6(j,i)+
+ & wturn6*fact(5)*gcorr6_turn(j,i)+
+ & wsccor*fact(2)*gsccorc(j,i)
+ gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
+ & wbond*gradbx(j,i)+
+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
+ & wsccor*fact(1)*gsccorx(j,i)
+ enddo
+#endif
+ enddo
+
+
+ do i=1,nres-3
+ gloc(i,icg)=gloc(i,icg)+wcorr*fact(3)*gcorr_loc(i)
+ & +wcorr5*fact(4)*g_corr5_loc(i)
+ & +wcorr6*fact(5)*g_corr6_loc(i)
+ & +wturn4*fact(3)*gel_loc_turn4(i)
+ & +wturn3*fact(2)*gel_loc_turn3(i)
+ & +wturn6*fact(5)*gel_loc_turn6(i)
+ & +wel_loc*fact(2)*gel_loc_loc(i)
+ & +wsccor*fact(1)*gsccor_loc(i)
+ enddo
+ endif
+ return
+ end
+C------------------------------------------------------------------------
+ subroutine enerprint(energia,fact)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ double precision energia(0:max_ene),fact(6)
+ etot=energia(0)
+ evdw=energia(1)+fact(6)*energia(21)
+#ifdef SCP14
+ evdw2=energia(2)+energia(17)
+#else
+ evdw2=energia(2)
+#endif
+ ees=energia(3)
+#ifdef SPLITELE
+ evdw1=energia(16)
+#endif
+ ecorr=energia(4)
+ ecorr5=energia(5)
+ ecorr6=energia(6)
+ eel_loc=energia(7)
+ eello_turn3=energia(8)
+ eello_turn4=energia(9)
+ eello_turn6=energia(10)
+ ebe=energia(11)
+ escloc=energia(12)
+ etors=energia(13)
+ etors_d=energia(14)
+ ehpb=energia(15)
+ esccor=energia(19)
+ edihcnstr=energia(20)
+ estr=energia(18)
+#ifdef SPLITELE
+ write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1,
+ & wvdwpp,
+ & estr,wbond,ebe,wang,escloc,wscloc,etors,wtor*fact(1),
+ & etors_d,wtor_d*fact(2),ehpb,wstrain,
+ & ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5),
+ & eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2),
+ & eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5),
+ & esccor,wsccor*fact(1),edihcnstr,ebr*nss,etot
+ 10 format (/'Virtual-chain energies:'//
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p elec)'/
+ & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/
+ & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
+ & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
+ & ' (SS bridges & dist. cnstr.)'/
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
+ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
+ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
+ & 'ETOT= ',1pE16.6,' (total)')
+#else
+ write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond,
+ & ebe,wang,escloc,wscloc,etors,wtor*fact(1),etors_d,wtor_d*fact2,
+ & ehpb,wstrain,ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),
+ & ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2),
+ & eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3),
+ & eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor,
+ & edihcnstr,ebr*nss,etot
+ 10 format (/'Virtual-chain energies:'//
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/
+ & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
+ & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
+ & ' (SS bridges & dist. cnstr.)'/
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
+ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
+ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
+ & 'ETOT= ',1pE16.6,' (total)')
+#endif
+ return
+ end
+C-----------------------------------------------------------------------
+ subroutine elj(evdw,evdw_t)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the LJ potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include "DIMENSIONS.COMPAR"
+ parameter (accur=1.0d-10)
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.TORSION'
+ include 'COMMON.ENEPS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CONTACTS'
+ dimension gg(3)
+ integer icant
+ external icant
+cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ evdw_t=0.0d0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+C Change 12/1/95
+ num_conti=0
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
+cd & 'iend=',iend(i,iint)
+ do j=istart(i,iint),iend(i,iint)
+ itypj=itype(j)
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+C Change 12/1/95 to calculate four-body interactions
+ rij=xj*xj+yj*yj+zj*zj
+ rrij=1.0D0/rij
+c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
+ eps0ij=eps(itypi,itypj)
+ fac=rrij**expon2
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=e1+e2
+ ij=icant(itypi,itypj)
+ eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
+cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
+cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
+ if (bb(itypi,itypj).gt.0.0d0) then
+ evdw=evdw+evdwij
+ else
+ evdw_t=evdw_t+evdwij
+ endif
+ if (calc_grad) then
+C
+C Calculate the components of the gradient in DC and X
+C
+ fac=-rrij*(e1+evdwij)
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ enddo
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ endif
+C
+C 12/1/95, revised on 5/20/97
+C
+C Calculate the contact function. The ith column of the array JCONT will
+C contain the numbers of atoms that make contacts with the atom I (of numbers
+C greater than I). The arrays FACONT and GACONT will contain the values of
+C the contact function and its derivative.
+C
+C Uncomment next line, if the correlation interactions include EVDW explicitly.
+c if (j.gt.i+1 .and. evdwij.le.0.0D0) then
+C Uncomment next line, if the correlation interactions are contact function only
+ if (j.gt.i+1.and. eps0ij.gt.0.0D0) then
+ rij=dsqrt(rij)
+ sigij=sigma(itypi,itypj)
+ r0ij=rs0(itypi,itypj)
+C
+C Check whether the SC's are not too far to make a contact.
+C
+ rcut=1.5d0*r0ij
+ call gcont(rij,rcut,1.0d0,0.2d0*rcut,fcont,fprimcont)
+C Add a new contact, if the SC's are close enough, but not too close (r<sigma).
+C
+ if (fcont.gt.0.0D0) then
+C If the SC-SC distance if close to sigma, apply spline.
+cAdam call gcont(-rij,-1.03d0*sigij,2.0d0*sigij,1.0d0,
+cAdam & fcont1,fprimcont1)
+cAdam fcont1=1.0d0-fcont1
+cAdam if (fcont1.gt.0.0d0) then
+cAdam fprimcont=fprimcont*fcont1+fcont*fprimcont1
+cAdam fcont=fcont*fcont1
+cAdam endif
+C Uncomment following 4 lines to have the geometric average of the epsilon0's
+cga eps0ij=1.0d0/dsqrt(eps0ij)
+cga do k=1,3
+cga gg(k)=gg(k)*eps0ij
+cga enddo
+cga eps0ij=-evdwij*eps0ij
+C Uncomment for AL's type of SC correlation interactions.
+cadam eps0ij=-evdwij
+ num_conti=num_conti+1
+ jcont(num_conti,i)=j
+ facont(num_conti,i)=fcont*eps0ij
+ fprimcont=eps0ij*fprimcont/rij
+ fcont=expon*fcont
+cAdam gacont(1,num_conti,i)=-fprimcont*xj+fcont*gg(1)
+cAdam gacont(2,num_conti,i)=-fprimcont*yj+fcont*gg(2)
+cAdam gacont(3,num_conti,i)=-fprimcont*zj+fcont*gg(3)
+C Uncomment following 3 lines for Skolnick's type of SC correlation.
+ gacont(1,num_conti,i)=-fprimcont*xj
+ gacont(2,num_conti,i)=-fprimcont*yj
+ gacont(3,num_conti,i)=-fprimcont*zj
+cd write (iout,'(2i5,2f10.5)') i,j,rij,facont(num_conti,i)
+cd write (iout,'(2i3,3f10.5)')
+cd & i,j,(gacont(kk,num_conti,i),kk=1,3)
+ endif
+ endif
+ enddo ! j
+ enddo ! iint
+C Change 12/1/95
+ num_cont(i)=num_conti
+ enddo ! i
+ if (calc_grad) then
+ do i=1,nct
+ do j=1,3
+ gvdwc(j,i)=expon*gvdwc(j,i)
+ gvdwx(j,i)=expon*gvdwx(j,i)
+ enddo
+ enddo
+ endif
+C******************************************************************************
+C
+C N O T E !!!
+C
+C To save time, the factor of EXPON has been extracted from ALL components
+C of GVDWC and GRADX. Remember to multiply them by this factor before further
+C use!
+C
+C******************************************************************************
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine eljk(evdw,evdw_t)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the LJK potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include "DIMENSIONS.COMPAR"
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ dimension gg(3)
+ logical scheck
+ integer icant
+ external icant
+c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ evdw_t=0.0d0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ itypj=itype(j)
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ fac_augm=rrij**expon
+ e_augm=augm(itypi,itypj)*fac_augm
+ r_inv_ij=dsqrt(rrij)
+ rij=1.0D0/r_inv_ij
+ r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
+ fac=r_shift_inv**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=e_augm+e1+e2
+ ij=icant(itypi,itypj)
+ eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm)
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps(itypi,itypj)
+cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
+cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
+cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
+ if (bb(itypi,itypj).gt.0.0d0) then
+ evdw=evdw+evdwij
+ else
+ evdw_t=evdw_t+evdwij
+ endif
+ if (calc_grad) then
+C
+C Calculate the components of the gradient in DC and X
+C
+ fac=-2.0D0*rrij*e_augm-r_inv_ij*r_shift_inv*(e1+e1+e2)
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ enddo
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ if (calc_grad) then
+ do i=1,nct
+ do j=1,3
+ gvdwc(j,i)=expon*gvdwc(j,i)
+ gvdwx(j,i)=expon*gvdwx(j,i)
+ enddo
+ enddo
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine ebp(evdw,evdw_t)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Berne-Pechukas potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include "DIMENSIONS.COMPAR"
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ common /srutu/ icall
+c double precision rrsave(maxdim)
+ logical lprn
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ evdw_t=0.0d0
+c print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
+c if (icall.eq.0) then
+c lprn=.true.
+c else
+ lprn=.false.
+c endif
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=vbld_inv(i+nres)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=vbld_inv(j+nres)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+cd if (icall.eq.0) then
+cd rrsave(ind)=rrij
+cd else
+cd rrij=rrsave(ind)
+cd endif
+ rij=dsqrt(rrij)
+C Calculate the angle-dependent terms of energy & contributions to derivatives.
+ call sc_angular
+C Calculate whole angle-dependent part of epsilon and contributions
+C to its derivatives
+ fac=(rrij*sigsq)**expon2
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ evdwij=evdwij*eps2rt*eps3rt
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj)
+ if (bb(itypi,itypj).gt.0.0d0) then
+ evdw=evdw+evdwij
+ else
+ evdw_t=evdw_t+evdwij
+ endif
+ if (calc_grad) then
+ if (lprn) then
+ sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
+cd & restyp(itypi),i,restyp(itypj),j,
+cd & epsi,sigm,chi1,chi2,chip1,chip2,
+cd & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
+cd & om1,om2,om12,1.0D0/dsqrt(rrij),
+cd & evdwij
+ endif
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)
+ sigder=fac/sigsq
+ fac=rrij*fac
+C Calculate radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate the angular part of the gradient and sum add the contributions
+C to the appropriate components of the Cartesian gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+c stop
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine egb(evdw,evdw_t)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Gay-Berne potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include "DIMENSIONS.COMPAR"
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ logical lprn
+ common /srutu/icall
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+ evdw=0.0D0
+ evdw_t=0.0d0
+ lprn=.false.
+c if (icall.gt.0) lprn=.true.
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=vbld_inv(i+nres)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=vbld_inv(j+nres)
+ sig0ij=sigma(itypi,itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+c write (iout,*) i,j,xj,yj,zj
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of energy and contributions to their
+C derivatives.
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+sig0ij
+C I hate to put IF's in the loops, but here don't have another choice!!!!
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
+ return
+ endif
+ sigder=-sig*sigsq
+c---------------------------------------------------------------
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ evdwij=evdwij*eps2rt*eps3rt
+ if (bb(itypi,itypj).gt.0) then
+ evdw=evdw+evdwij
+ else
+ evdw_t=evdw_t+evdwij
+ endif
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
+c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
+c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
+c & aux*e2/eps(itypi,itypj)
+ if (lprn) then
+ sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+ & restyp(itypi),i,restyp(itypj),j,
+ & epsi,sigm,chi1,chi2,chip1,chip2,
+ & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
+ & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+ & evdwij
+ endif
+ if (calc_grad) then
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac
+C Calculate the radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate angular part of the gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine egbv(evdw,evdw_t)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Gay-Berne-Vorobjev potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include "DIMENSIONS.COMPAR"
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ common /srutu/ icall
+ logical lprn
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ evdw_t=0.0d0
+c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+ evdw=0.0D0
+ lprn=.false.
+c if (icall.gt.0) lprn=.true.
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=vbld_inv(i+nres)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=vbld_inv(j+nres)
+ sig0ij=sigma(itypi,itypj)
+ r0ij=r0(itypi,itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of energy and contributions to their
+C derivatives.
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+r0ij
+C I hate to put IF's in the loops, but here don't have another choice!!!!
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
+ return
+ endif
+ sigder=-sig*sigsq
+c---------------------------------------------------------------
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ fac_augm=rrij**expon
+ e_augm=augm(itypi,itypj)*fac_augm
+ evdwij=evdwij*eps2rt*eps3rt
+ if (bb(itypi,itypj).gt.0.0d0) then
+ evdw=evdw+evdwij+e_augm
+ else
+ evdw_t=evdw_t+evdwij+e_augm
+ endif
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+aux*(e1+e_augm)
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
+c eneps_temp(ij)=eneps_temp(ij)
+c & +(evdwij+e_augm)/eps(itypi,itypj)
+c if (lprn) then
+c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+c epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+c & restyp(itypi),i,restyp(itypj),j,
+c & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
+c & chi1,chi2,chip1,chip2,
+c & eps1,eps2rt**2,eps3rt**2,
+c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+c & evdwij+e_augm
+c endif
+ if (calc_grad) then
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac-2*expon*rrij*e_augm
+C Calculate the radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate angular part of the gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ return
+ end
+C-----------------------------------------------------------------------------
+
+
+ SUBROUTINE emomo(evdw,evdw_p,evdw_m)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Gay-Berne potential of interaction.
+C
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ logical lprn
+ double precision scalar
+ double precision ener(4)
+ integer troll,iint
+
+ IF (energy_dec) write (iout,'(a)')
+ & ' AAi i AAj j 1/rij Rtail Rhead evdwij Fcav Ecl
+ & Egb Epol Fisocav Elj Equad evdw'
+ evdw = 0.0D0
+ evdw_p = 0.0D0
+ evdw_m = 0.0D0
+c DIAGNOSTICS
+ccccc energy_dec=.false.
+c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+c lprn = .false.
+c if (icall.eq.0) lprn=.false.
+c END DIAGNOSTICS
+c ind = 0
+ DO i = iatsc_s, iatsc_e
+ itypi = itype(i)
+c itypi1 = itype(i+1)
+ dxi = dc_norm(1,nres+i)
+ dyi = dc_norm(2,nres+i)
+ dzi = dc_norm(3,nres+i)
+c dsci_inv=dsc_inv(itypi)
+ dsci_inv = vbld_inv(i+nres)
+c DO k = 1, 3
+c ctail(k,1) = c(k, i+nres)
+c & - dtail(1,itypi,itypj) * dc_norm(k, nres+i)
+c END DO
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+c!-------------------------------------------------------------------
+C Calculate SC interaction energy.
+ DO iint = 1, nint_gr(i)
+ DO j = istart(i,iint), iend(i,iint)
+c! initialize variables for electrostatic gradients
+ CALL elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+c ind=ind+1
+c dscj_inv = dsc_inv(itypj)
+ dscj_inv = vbld_inv(j+nres)
+c! rij holds 1/(distance of Calpha atoms)
+ rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
+ rij = dsqrt(rrij)
+c!-------------------------------------------------------------------
+C Calculate angle-dependent terms of energy and contributions to their
+C derivatives.
+
+#IFDEF CHECK_MOMO
+c! DO troll = 10, 5000
+c! om1 = 0.0d0
+c! om2 = 0.0d0
+c! om12 = 1.0d0
+c! sqom1 = om1 * om1
+c! sqom2 = om2 * om2
+c! sqom12 = om12 * om12
+c! rij = 5.0d0 / troll
+c! rrij = rij * rij
+c! Rtail = troll / 5.0d0
+c! Rhead = troll / 5.0d0
+c! Rhead = dsqrt((Rtail**2)+((dabs(d1-d2))**2))
+c! Rtail = dsqrt((Rtail**2)
+c! & +((dabs(dtail(1,itypi,itypj)-dtail(2,itypi,itypj)))**2))
+c! rij = 1.0d0/Rtail
+c! rrij = rij * rij
+#ENDIF
+ CALL sc_angular
+c! this should be in elgrad_init but om's are calculated by sc_angular
+c! which in turn is used by older potentials
+c! which proves how tangled UNRES code is >.<
+c! om = omega, sqom = om^2
+ sqom1 = om1 * om1
+ sqom2 = om2 * om2
+ sqom12 = om12 * om12
+
+c! now we calculate EGB - Gey-Berne
+c! It will be summed up in evdwij and saved in evdw
+ sigsq = 1.0D0 / sigsq
+ sig = sig0ij * dsqrt(sigsq)
+c! rij_shift = 1.0D0 / rij - sig + sig0ij
+ rij_shift = Rtail - sig + sig0ij
+c write (2,*) "Rtal",Rtail," sig",sig," sigsq",sigsq,
+c & " sig0ij",sig0ij
+c write (2,*) "rij_shift",rij_shift
+ IF (rij_shift.le.0.0D0) THEN
+ evdw = 1.0D20
+ RETURN
+ END IF
+ sigder = -sig * sigsq
+ rij_shift = 1.0D0 / rij_shift
+ fac = rij_shift**expon
+ c1 = fac * fac * aa(itypi,itypj)
+#ifdef SCALREP
+! Scale down the repulsive term for 1,4 interactions.
+ if (iabs(j-i).le.4) c1 = 0.01d0 * c1
+#endif
+c! c1 = 0.0d0
+ c2 = fac * bb(itypi,itypj)
+c! c2 = 0.0d0
+c write (2,*) "eps1",eps1," eps2rt",eps2rt," eps3rt",eps3rt,
+c & " c1",c1," c2",c2
+ evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+ eps2der = eps3rt * evdwij
+ eps3der = eps2rt * evdwij
+c! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij
+ evdwij = eps2rt * eps3rt * evdwij
+c! evdwij = 0.0d0
+c! write (*,*) "Gey Berne = ", evdwij
+#ifdef TSCSC
+ IF (bb(itypi,itypj).gt.0) THEN
+ evdw_p = evdw_p + evdwij
+ ELSE
+ evdw_m = evdw_m + evdwij
+ END IF
+#else
+ evdw = evdw
+ & + evdwij
+#endif
+c!-------------------------------------------------------------------
+c! Calculate some components of GGB
+ c1 = c1 * eps1 * eps2rt**2 * eps3rt**2
+ fac = -expon * (c1 + evdwij) * rij_shift
+ sigder = fac * sigder
+c! fac = rij * fac
+c! Calculate distance derivative
+c! gg(1) = xj * fac
+c! gg(2) = yj * fac
+c! gg(3) = zj * fac
+ gg(1) = fac
+ gg(2) = fac
+ gg(3) = fac
+c! write (*,*) "gg(1) = ", gg(1)
+c! write (*,*) "gg(2) = ", gg(2)
+c! write (*,*) "gg(3) = ", gg(3)
+c! The angular derivatives of GGB are brought together in sc_grad
+c!-------------------------------------------------------------------
+c! Fcav
+c!
+c! Catch gly-gly interactions to skip calculation of something that
+c! does not exist
+
+ IF (itypi.eq.10.and.itypj.eq.10) THEN
+ Fcav = 0.0d0
+ dFdR = 0.0d0
+ dCAVdOM1 = 0.0d0
+ dCAVdOM2 = 0.0d0
+ dCAVdOM12 = 0.0d0
+ ELSE
+
+c! we are not 2 glycines, so we calculate Fcav (and maybe more)
+ fac = chis1 * sqom1 + chis2 * sqom2
+ & - 2.0d0 * chis12 * om1 * om2 * om12
+c! we will use pom later in Gcav, so dont mess with it!
+ pom = 1.0d0 - chis1 * chis2 * sqom12
+
+ Lambf = (1.0d0 - (fac / pom))
+ Lambf = dsqrt(Lambf)
+
+
+ sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+c! write (*,*) "sparrow = ", sparrow
+ Chif = Rtail * sparrow
+ ChiLambf = Chif * Lambf
+ eagle = dsqrt(ChiLambf)
+ bat = ChiLambf ** 11.0d0
+
+ top = b1 * ( eagle + b2 * ChiLambf - b3 )
+ bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0)
+ botsq = bot * bot
+
+c! write (*,*) "sig1 = ",sig1
+c! write (*,*) "sig2 = ",sig2
+c! write (*,*) "Rtail = ",Rtail
+c! write (*,*) "sparrow = ",sparrow
+c! write (*,*) "Chis1 = ", chis1
+c! write (*,*) "Chis2 = ", chis2
+c! write (*,*) "Chis12 = ", chis12
+c! write (*,*) "om1 = ", om1
+c! write (*,*) "om2 = ", om2
+c! write (*,*) "om12 = ", om12
+c! write (*,*) "sqom1 = ", sqom1
+c! write (*,*) "sqom2 = ", sqom2
+c! write (*,*) "sqom12 = ", sqom12
+c! write (*,*) "Lambf = ",Lambf
+c! write (*,*) "b1 = ",b1
+c! write (*,*) "b2 = ",b2
+c! write (*,*) "b3 = ",b3
+c! write (*,*) "b4 = ",b4
+c! write (*,*) "top = ",top
+c! write (*,*) "bot = ",bot
+ Fcav = top / bot
+c! Fcav = 0.0d0
+c! write (*,*) "Fcav = ", Fcav
+c!-------------------------------------------------------------------
+c! derivative of Fcav is Gcav...
+c!---------------------------------------------------
+
+ dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf))
+ dbot = 12.0d0 * b4 * bat * Lambf
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+c! dFdR = 0.0d0
+c! write (*,*) "dFcav/dR = ", dFdR
+
+ dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif))
+ dbot = 12.0d0 * b4 * bat * Chif
+ eagle = Lambf * pom
+ dFdOM1 = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+ dFdOM2 = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
+ dFdOM12 = chis12 * (chis1 * om1 * om12 - om2)
+ & * (chis2 * om2 * om12 - om1) / (eagle * pom)
+
+ dFdL = ((dtop * bot - top * dbot) / botsq)
+c! dFdL = 0.0d0
+ dCAVdOM1 = dFdL * ( dFdOM1 )
+ dCAVdOM2 = dFdL * ( dFdOM2 )
+ dCAVdOM12 = dFdL * ( dFdOM12 )
+c! write (*,*) "dFcav/dOM1 = ", dCAVdOM1
+c! write (*,*) "dFcav/dOM2 = ", dCAVdOM2
+c! write (*,*) "dFcav/dOM12 = ", dCAVdOM12
+c! write (*,*) ""
+c!-------------------------------------------------------------------
+c! Finally, add the distance derivatives of GB and Fcav to gvdwc
+c! Pom is used here to project the gradient vector into
+c! cartesian coordinates and at the same time contains
+c! dXhb/dXsc derivative (for charged amino acids
+c! location of hydrophobic centre of interaction is not
+c! the same as geometric centre of side chain, this
+c! derivative takes that into account)
+c! derivatives of omega angles will be added in sc_grad
+
+ DO k= 1, 3
+ ertail(k) = Rtail_distance(k)/Rtail
+ END DO
+ erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
+ erdxj = scalar( ertail(1), dC_norm(1,j+nres) )
+ facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+ facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+ DO k = 1, 3
+c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
+c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
+ pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+ gvdwx(k,i) = gvdwx(k,i)
+ & - (( dFdR + gg(k) ) * pom)
+c! & - ( dFdR * pom )
+ pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + (( dFdR + gg(k) ) * pom)
+c! & + ( dFdR * pom )
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - (( dFdR + gg(k) ) * ertail(k))
+c! & - ( dFdR * ertail(k))
+
+ gvdwc(k,j) = gvdwc(k,j)
+ & + (( dFdR + gg(k) ) * ertail(k))
+c! & + ( dFdR * ertail(k))
+
+ gg(k) = 0.0d0
+c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
+c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
+ END DO
+
+c!-------------------------------------------------------------------
+c! Compute head-head and head-tail energies for each state
+
+ isel = iabs(Qi) + iabs(Qj)
+ IF (isel.eq.0) THEN
+c! No charges - do nothing
+ eheadtail = 0.0d0
+
+ ELSE IF (isel.eq.4) THEN
+c! Calculate dipole-dipole interactions
+ CALL edd(ecl)
+ eheadtail = ECL
+
+ ELSE IF (isel.eq.1 .and. iabs(Qi).eq.1) THEN
+c! Charge-nonpolar interactions
+ CALL eqn(epol)
+ eheadtail = epol
+
+ ELSE IF (isel.eq.1 .and. iabs(Qj).eq.1) THEN
+c! Nonpolar-charge interactions
+ CALL enq(epol)
+ eheadtail = epol
+
+ ELSE IF (isel.eq.3 .and. icharge(itypj).eq.2) THEN
+c! Charge-dipole interactions
+ CALL eqd(ecl, elj, epol)
+ eheadtail = ECL + elj + epol
+
+ ELSE IF (isel.eq.3 .and. icharge(itypi).eq.2) THEN
+c! Dipole-charge interactions
+ CALL edq(ecl, elj, epol)
+ eheadtail = ECL + elj + epol
+
+ ELSE IF ((isel.eq.2.and.
+ & iabs(Qi).eq.1).and.
+ & nstate(itypi,itypj).eq.1) THEN
+c! Same charge-charge interaction ( +/+ or -/- )
+ CALL eqq(Ecl,Egb,Epol,Fisocav,Elj)
+ eheadtail = ECL + Egb + Epol + Fisocav + Elj
+
+ ELSE IF ((isel.eq.2.and.
+ & iabs(Qi).eq.1).and.
+ & nstate(itypi,itypj).ne.1) THEN
+c! Different charge-charge interaction ( +/- or -/+ )
+ CALL energy_quad
+ & (istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
+ END IF
+ END IF ! this endif ends the "catch the gly-gly" at the beggining of Fcav
+c! write (*,*) "evdw = ", evdw
+c! write (*,*) "Fcav = ", Fcav
+c! write (*,*) "eheadtail = ", eheadtail
+ evdw = evdw
+ & + Fcav
+ & + eheadtail
+
+ IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)')
+ & restyp(itype(i)),i,restyp(itype(j)),j,
+ & 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,
+ & Equad,evdwij+Fcav+eheadtail,evdw
+c IF (energy_dec) write (*,'(2(1x,a3,i3),3f6.2,9f16.7)')
+c & restyp(itype(i)),i,restyp(itype(j)),j,
+c & 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,
+c & Equad,evdwij+Fcav+eheadtail,evdw
+#IFDEF CHECK_MOMO
+ evdw = 0.0d0
+ END DO ! troll
+#ENDIF
+
+c!-------------------------------------------------------------------
+c! As all angular derivatives are done, now we sum them up,
+c! then transform and project into cartesian vectors and add to gvdwc
+c! We call sc_grad always, with the exception of +/- interaction.
+c! This is because energy_quad subroutine needs to handle
+c! this job in his own way.
+c! This IS probably not very efficient and SHOULD be optimised
+c! but it will require major restructurization of emomo
+c! so it will be left as it is for now
+c! write (*,*) 'troll1, nstate =', nstate (itypi,itypj)
+ IF (nstate(itypi,itypj).eq.1) THEN
+#ifdef TSCSC
+ IF (bb(itypi,itypj).gt.0) THEN
+ CALL sc_grad
+ ELSE
+ CALL sc_grad_T
+ END IF
+#else
+ CALL sc_grad
+#endif
+ END IF
+c!-------------------------------------------------------------------
+c! NAPISY KONCOWE
+ END DO ! j
+ END DO ! iint
+ END DO ! i
+ if (energy_dec) write (iout,*) "evdw before exiting emomo:",evdw
+c write (iout,*) "Number of loop steps in EGB:",ind
+c energy_dec=.false.
+ RETURN
+ END SUBROUTINE emomo
+c! END OF MOMO
+
+
+C-----------------------------------------------------------------------------
+
+
+ SUBROUTINE eqq(Ecl,Egb,Epol,Fisocav,Elj)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar, facd3, facd4, federmaus, adler
+c! Epol and Gpol analytical parameters
+ alphapol1 = alphapol(itypi,itypj)
+ alphapol2 = alphapol(itypj,itypi)
+c! Fisocav and Gisocav analytical parameters
+ al1 = alphiso(1,itypi,itypj)
+ al2 = alphiso(2,itypi,itypj)
+ al3 = alphiso(3,itypi,itypj)
+ al4 = alphiso(4,itypi,itypj)
+ csig = (1.0d0
+ & / dsqrt(sigiso1(itypi, itypj)**2.0d0
+ & + sigiso2(itypi,itypj)**2.0d0))
+c!
+ pis = sig0head(itypi,itypj)
+ eps_head = epshead(itypi,itypj)
+ Rhead_sq = Rhead * Rhead
+c! R1 - distance between head of ith side chain and tail of jth sidechain
+c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R1 = 0.0d0
+ R2 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances needed by Epol
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+c! Pitagoras
+ R1 = dsqrt(R1)
+ R2 = dsqrt(R2)
+
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,1,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,1,itypi,itypj))**2))
+
+c!-------------------------------------------------------------------
+c! Coulomb electrostatic interaction
+ Ecl = (332.0d0 * Qij) / Rhead
+c! derivative of Ecl is Gcl...
+ dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+c!-------------------------------------------------------------------
+c! Generalised Born Solvent Polarization
+c! Charged head polarizes the solvent
+ ee = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
+ Fgb = sqrt( ( Rhead_sq ) + a12sq * ee)
+ Egb = -(332.0d0 * Qij * eps_inout_fac) / Fgb
+c! Derivative of Egb is Ggb...
+ dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
+ dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee) ) )
+ & / ( 2.0d0 * Fgb )
+ dGGBdR = dGGBdFGB * dFGBdR
+c!-------------------------------------------------------------------
+c! Fisocav - isotropic cavity creation term
+c! or "how much energy it costs to put charged head in water"
+ pom = Rhead * csig
+ top = al1 * (dsqrt(pom) + al2 * pom - al3)
+ bot = (1.0d0 + al4 * pom**12.0d0)
+ botsq = bot * bot
+ FisoCav = top / bot
+c! write (*,*) "Rhead = ",Rhead
+c! write (*,*) "csig = ",csig
+c! write (*,*) "pom = ",pom
+c! write (*,*) "al1 = ",al1
+c! write (*,*) "al2 = ",al2
+c! write (*,*) "al3 = ",al3
+c! write (*,*) "al4 = ",al4
+c! write (*,*) "top = ",top
+c! write (*,*) "bot = ",bot
+c! Derivative of Fisocav is GCV...
+ dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
+ dbot = 12.0d0 * al4 * pom ** 11.0d0
+ dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+c!-------------------------------------------------------------------
+c! Epol
+c! Polarization energy - charged heads polarize hydrophobic "neck"
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR1 = ( R1 * R1 ) / MomoFac1
+ RR2 = ( R2 * R2 ) / MomoFac2
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ ee2 = exp(-( RR2 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1 )
+ fgb2 = sqrt( RR2 + a12sq * ee2 )
+ epol = 332.0d0 * eps_inout_fac * (
+ & (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
+c! epol = 0.0d0
+c write (*,*) "eps_inout_fac = ",eps_inout_fac
+c write (*,*) "alphapol1 = ", alphapol1
+c write (*,*) "alphapol2 = ", alphapol2
+c write (*,*) "fgb1 = ", fgb1
+c write (*,*) "fgb2 = ", fgb2
+c write (*,*) "epol = ", epol
+c! derivative of Epol is Gpol...
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)
+ & / (fgb1 ** 5.0d0)
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)
+ & / (fgb2 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1)
+ & * ( 2.0d0 - (0.5d0 * ee1) ) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdR2 = ( (R2 / MomoFac2)
+ & * ( 2.0d0 - (0.5d0 * ee2) ) )
+ & / ( 2.0d0 * fgb2 )
+ dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))
+ & * ( 2.0d0 - 0.5d0 * ee1) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))
+ & * ( 2.0d0 - 0.5d0 * ee2) )
+ & / ( 2.0d0 * fgb2 )
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1
+c! dPOLdR1 = 0.0d0
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2
+c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+c! dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Elj
+c! Lennard-Jones 6-12 interaction between heads
+ pom = (pis / Rhead)**6.0d0
+ Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+c! derivative of Elj is Glj
+ dGLJdR = 4.0d0 * eps_head
+ & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))
+ & + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+c!-------------------------------------------------------------------
+c! Return the results
+c! These things do the dRdX derivatives, that is
+c! allow us to change what we see from function that changes with
+c! distance to function that changes with LOCATION (of the interaction
+c! site)
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+ facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+
+c! Now we add appropriate partial derivatives (one in each dimension)
+ DO k = 1, 3
+ hawk = (erhead_tail(k,1) +
+ & facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+ condor = (erhead_tail(k,2) +
+ & facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dGCLdR * pom
+ & - dGGBdR * pom
+ & - dGCVdR * pom
+ & - dPOLdR1 * hawk
+ & - dPOLdR2 * (erhead_tail(k,2)
+ & -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
+ & - dGLJdR * pom
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dGCLdR * pom
+ & + dGGBdR * pom
+ & + dGCVdR * pom
+ & + dPOLdR1 * (erhead_tail(k,1)
+ & -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
+ & + dPOLdR2 * condor
+ & + dGLJdR * pom
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dGCLdR * erhead(k)
+ & - dGGBdR * erhead(k)
+ & - dGCVdR * erhead(k)
+ & - dPOLdR1 * erhead_tail(k,1)
+ & - dPOLdR2 * erhead_tail(k,2)
+ & - dGLJdR * erhead(k)
+
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dGCLdR * erhead(k)
+ & + dGGBdR * erhead(k)
+ & + dGCVdR * erhead(k)
+ & + dPOLdR1 * erhead_tail(k,1)
+ & + dPOLdR2 * erhead_tail(k,2)
+ & + dGLJdR * erhead(k)
+
+ END DO
+ RETURN
+ END SUBROUTINE eqq
+c!-------------------------------------------------------------------
+ SUBROUTINE energy_quad
+ &(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar
+ double precision ener(4)
+ double precision dcosom1(3),dcosom2(3)
+c! used in Epol derivatives
+ double precision facd3, facd4
+ double precision federmaus, adler
+c! Epol and Gpol analytical parameters
+ alphapol1 = alphapol(itypi,itypj)
+ alphapol2 = alphapol(itypj,itypi)
+c! Fisocav and Gisocav analytical parameters
+ al1 = alphiso(1,itypi,itypj)
+ al2 = alphiso(2,itypi,itypj)
+ al3 = alphiso(3,itypi,itypj)
+ al4 = alphiso(4,itypi,itypj)
+ csig = (1.0d0
+ & / dsqrt(sigiso1(itypi, itypj)**2.0d0
+ & + sigiso2(itypi,itypj)**2.0d0))
+c!
+ w1 = wqdip(1,itypi,itypj)
+ w2 = wqdip(2,itypi,itypj)
+ pis = sig0head(itypi,itypj)
+ eps_head = epshead(itypi,itypj)
+c! First things first:
+c! We need to do sc_grad's job with GB and Fcav
+ eom1 =
+ & eps2der * eps2rt_om1
+ & - 2.0D0 * alf1 * eps3der
+ & + sigder * sigsq_om1
+ & + dCAVdOM1
+ eom2 =
+ & eps2der * eps2rt_om2
+ & + 2.0D0 * alf2 * eps3der
+ & + sigder * sigsq_om2
+ & + dCAVdOM2
+ eom12 =
+ & evdwij * eps1_om12
+ & + eps2der * eps2rt_om12
+ & - 2.0D0 * alf12 * eps3der
+ & + sigder *sigsq_om12
+ & + dCAVdOM12
+c! now some magical transformations to project gradient into
+c! three cartesian vectors
+ DO k = 1, 3
+ dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+ dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+ gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
+c! this acts on hydrophobic center of interaction
+ gvdwx(k,i)= gvdwx(k,i) - gg(k)
+ & + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
+ & + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+ gvdwx(k,j)= gvdwx(k,j) + gg(k)
+ & + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
+ & + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+c! this acts on Calpha
+ gvdwc(k,i)=gvdwc(k,i)-gg(k)
+ gvdwc(k,j)=gvdwc(k,j)+gg(k)
+ END DO
+c! sc_grad is done, now we will compute
+ eheadtail = 0.0d0
+ eom1 = 0.0d0
+ eom2 = 0.0d0
+ eom12 = 0.0d0
+
+c! ENERGY DEBUG
+c! ii = 1
+c! jj = 1
+c! d1 = dhead(1, 1, itypi, itypj)
+c! d2 = dhead(2, 1, itypi, itypj)
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,ii,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,jj,itypi,itypj))**2))
+c! Rhead = dsqrt((Rtail**2)+((dabs(d1-d2))**2))
+c! END OF ENERGY DEBUG
+c*************************************************************
+ DO istate = 1, nstate(itypi,itypj)
+c*************************************************************
+ IF (istate.ne.1) THEN
+ IF (istate.lt.3) THEN
+ ii = 1
+ ELSE
+ ii = 2
+ END IF
+ jj = istate/ii
+ d1 = dhead(1,ii,itypi,itypj)
+ d2 = dhead(2,jj,itypi,itypj)
+ DO k = 1,3
+ chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+ chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+ Rhead_distance(k) = chead(k,2) - chead(k,1)
+ END DO
+c! pitagoras (root of sum of squares)
+ Rhead = dsqrt(
+ & (Rhead_distance(1)*Rhead_distance(1))
+ & + (Rhead_distance(2)*Rhead_distance(2))
+ & + (Rhead_distance(3)*Rhead_distance(3)))
+ END IF
+ Rhead_sq = Rhead * Rhead
+
+c! R1 - distance between head of ith side chain and tail of jth sidechain
+c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R1 = 0.0d0
+ R2 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+c! Pitagoras
+ R1 = dsqrt(R1)
+ R2 = dsqrt(R2)
+
+c! ENERGY DEBUG
+c! write (*,*) "istate = ", istate
+c! write (*,*) "ii = ", ii
+c! write (*,*) "jj = ", jj
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,ii,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,jj,itypi,itypj))**2))
+c! Rhead = dsqrt((Rtail**2)+((dabs(d1-d2))**2))
+c! Rhead_sq = Rhead * Rhead
+c! write (*,*) "d1 = ",d1
+c! write (*,*) "d2 = ",d2
+c! write (*,*) "R1 = ",R1
+c! write (*,*) "R2 = ",R2
+c! write (*,*) "Rhead = ",Rhead
+c! END OF ENERGY DEBUG
+
+c!-------------------------------------------------------------------
+c! Coulomb electrostatic interaction
+ Ecl = (332.0d0 * Qij) / (Rhead * eps_in)
+c! Ecl = 0.0d0
+c! write (*,*) "Ecl = ", Ecl
+c! derivative of Ecl is Gcl...
+ dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
+c! dGCLdR = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+c!-------------------------------------------------------------------
+c! Generalised Born Solvent Polarization
+ ee = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
+ Fgb = sqrt( ( Rhead_sq ) + a12sq * ee)
+ Egb = -(332.0d0 * Qij * eps_inout_fac) / Fgb
+c! Egb = 0.0d0
+c! write (*,*) "a1*a2 = ", a12sq
+c! write (*,*) "Rhead = ", Rhead
+c! write (*,*) "Rhead_sq = ", Rhead_sq
+c! write (*,*) "ee = ", ee
+c! write (*,*) "Fgb = ", Fgb
+c! write (*,*) "fac = ", eps_inout_fac
+c! write (*,*) "Qij = ", Qij
+c! write (*,*) "Egb = ", Egb
+c! Derivative of Egb is Ggb...
+c! dFGBdR is used by Quad's later...
+ dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
+ dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee) ) )
+ & / ( 2.0d0 * Fgb )
+ dGGBdR = dGGBdFGB * dFGBdR
+c! dGGBdR = 0.0d0
+c!-------------------------------------------------------------------
+c! Fisocav - isotropic cavity creation term
+ pom = Rhead * csig
+ top = al1 * (dsqrt(pom) + al2 * pom - al3)
+ bot = (1.0d0 + al4 * pom**12.0d0)
+ botsq = bot * bot
+ FisoCav = top / bot
+c! FisoCav = 0.0d0
+c! write (*,*) "pom = ",pom
+c! write (*,*) "al1 = ",al1
+c! write (*,*) "al2 = ",al2
+c! write (*,*) "al3 = ",al3
+c! write (*,*) "al4 = ",al4
+c! write (*,*) "top = ",top
+c! write (*,*) "bot = ",bot
+c! write (*,*) "Fisocav = ", Fisocav
+
+c! Derivative of Fisocav is GCV...
+ dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
+ dbot = 12.0d0 * al4 * pom ** 11.0d0
+ dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+c! dGCVdR = 0.0d0
+c!-------------------------------------------------------------------
+c! Polarization energy
+c! Epol
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR1 = ( R1 * R1 ) / MomoFac1
+ RR2 = ( R2 * R2 ) / MomoFac2
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ ee2 = exp(-( RR2 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1 )
+ fgb2 = sqrt( RR2 + a12sq * ee2 )
+ epol = 332.0d0 * eps_inout_fac * (
+ & (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
+c! epol = 0.0d0
+c! derivative of Epol is Gpol...
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)
+ & / (fgb1 ** 5.0d0)
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)
+ & / (fgb2 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1)
+ & * ( 2.0d0 - (0.5d0 * ee1) ) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdR2 = ( (R2 / MomoFac2)
+ & * ( 2.0d0 - (0.5d0 * ee2) ) )
+ & / ( 2.0d0 * fgb2 )
+ dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))
+ & * ( 2.0d0 - 0.5d0 * ee1) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))
+ & * ( 2.0d0 - 0.5d0 * ee2) )
+ & / ( 2.0d0 * fgb2 )
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1
+c! dPOLdR1 = 0.0d0
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2
+c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+c! dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Elj
+ pom = (pis / Rhead)**6.0d0
+ Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+c! Elj = 0.0d0
+c! derivative of Elj is Glj
+ dGLJdR = 4.0d0 * eps_head
+ & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))
+ & + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+c! dGLJdR = 0.0d0
+c!-------------------------------------------------------------------
+c! Equad
+ IF (Wqd.ne.0.0d0) THEN
+ Beta1 = 5.0d0 + 3.0d0 * (sqom12 - 1.0d0)
+ & - 37.5d0 * ( sqom1 + sqom2 )
+ & + 157.5d0 * ( sqom1 * sqom2 )
+ & - 45.0d0 * om1*om2*om12
+ fac = -( Wqd / (2.0d0 * Fgb**5.0d0) )
+ Equad = fac * Beta1
+c! Equad = 0.0d0
+c! derivative of Equad...
+ dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
+c! dQUADdR = 0.0d0
+ dQUADdOM1 = fac
+ & * (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
+c! dQUADdOM1 = 0.0d0
+ dQUADdOM2 = fac
+ & * (-75.0d0*om2 + 315.0d0*sqom1*om2 - 45.0d0*om1*om12)
+c! dQUADdOM2 = 0.0d0
+ dQUADdOM12 = fac
+ & * ( 6.0d0*om12 - 45.0d0*om1*om2 )
+c! dQUADdOM12 = 0.0d0
+ ELSE
+ Beta1 = 0.0d0
+ Equad = 0.0d0
+ END IF
+c!-------------------------------------------------------------------
+c! Return the results
+c! Angular stuff
+ eom1 = dPOLdOM1 + dQUADdOM1
+ eom2 = dPOLdOM2 + dQUADdOM2
+ eom12 = dQUADdOM12
+c! now some magical transformations to project gradient into
+c! three cartesian vectors
+ DO k = 1, 3
+ dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
+ dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
+ tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
+ END DO
+c! Radial stuff
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+ facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+c! Throw the results into gheadtail which holds gradients
+c! for each micro-state
+ DO k = 1, 3
+ hawk = erhead_tail(k,1) +
+ & facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))
+ condor = erhead_tail(k,2) +
+ & facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+c! this acts on hydrophobic center of interaction
+ gheadtail(k,1,1) = gheadtail(k,1,1)
+ & - dGCLdR * pom
+ & - dGGBdR * pom
+ & - dGCVdR * pom
+ & - dPOLdR1 * hawk
+ & - dPOLdR2 * (erhead_tail(k,2)
+ & -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
+ & - dGLJdR * pom
+ & - dQUADdR * pom
+ & - tuna(k)
+ & + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
+ & + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+c! this acts on hydrophobic center of interaction
+ gheadtail(k,2,1) = gheadtail(k,2,1)
+ & + dGCLdR * pom
+ & + dGGBdR * pom
+ & + dGCVdR * pom
+ & + dPOLdR1 * (erhead_tail(k,1)
+ & -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
+ & + dPOLdR2 * condor
+ & + dGLJdR * pom
+ & + dQUADdR * pom
+ & + tuna(k)
+ & + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
+ & + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+
+c! this acts on Calpha
+ gheadtail(k,3,1) = gheadtail(k,3,1)
+ & - dGCLdR * erhead(k)
+ & - dGGBdR * erhead(k)
+ & - dGCVdR * erhead(k)
+ & - dPOLdR1 * erhead_tail(k,1)
+ & - dPOLdR2 * erhead_tail(k,2)
+ & - dGLJdR * erhead(k)
+ & - dQUADdR * erhead(k)
+ & - tuna(k)
+
+c! this acts on Calpha
+ gheadtail(k,4,1) = gheadtail(k,4,1)
+ & + dGCLdR * erhead(k)
+ & + dGGBdR * erhead(k)
+ & + dGCVdR * erhead(k)
+ & + dPOLdR1 * erhead_tail(k,1)
+ & + dPOLdR2 * erhead_tail(k,2)
+ & + dGLJdR * erhead(k)
+ & + dQUADdR * erhead(k)
+ & + tuna(k)
+ END DO
+c! write(*,*) "ECL = ", Ecl
+c! write(*,*) "Egb = ", Egb
+c! write(*,*) "Epol = ", Epol
+c! write(*,*) "Fisocav = ", Fisocav
+c! write(*,*) "Elj = ", Elj
+c! write(*,*) "Equad = ", Equad
+c! write(*,*) "wstate = ", wstate(istate,itypi,itypj)
+c! write(*,*) "eheadtail = ", eheadtail
+c! write(*,*) "TROLL = ", dexp(-betaT * ener(istate))
+c! write(*,*) "dGCLdR = ", dGCLdR
+c! write(*,*) "dGGBdR = ", dGGBdR
+c! write(*,*) "dGCVdR = ", dGCVdR
+c! write(*,*) "dPOLdR1 = ", dPOLdR1
+c! write(*,*) "dPOLdR2 = ", dPOLdR2
+c! write(*,*) "dGLJdR = ", dGLJdR
+c! write(*,*) "dQUADdR = ", dQUADdR
+c! write(*,*) "tuna(",k,") = ", tuna(k)
+ ener(istate) = ECL + Egb + Epol + Fisocav + Elj + Equad
+ eheadtail = eheadtail
+ & + wstate(istate, itypi, itypj)
+ & * dexp(-betaT * ener(istate))
+c! foreach cartesian dimension
+ DO k = 1, 3
+c! foreach of two gvdwx and gvdwc
+ DO l = 1, 4
+ gheadtail(k,l,2) = gheadtail(k,l,2)
+ & + wstate( istate, itypi, itypj )
+ & * dexp(-betaT * ener(istate))
+ & * gheadtail(k,l,1)
+ gheadtail(k,l,1) = 0.0d0
+ END DO
+ END DO
+ END DO
+c! Here ended the gigantic DO istate = 1, 4, which starts
+c! at the beggining of the subroutine
+
+ DO k = 1, 3
+ DO l = 1, 4
+ gheadtail(k,l,2) = gheadtail(k,l,2) / eheadtail
+ END DO
+ gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)
+ gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)
+ gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)
+ gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)
+ DO l = 1, 4
+ gheadtail(k,l,1) = 0.0d0
+ gheadtail(k,l,2) = 0.0d0
+ END DO
+ END DO
+ eheadtail = (-dlog(eheadtail)) / betaT
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ dQUADdOM1 = 0.0d0
+ dQUADdOM2 = 0.0d0
+ dQUADdOM12 = 0.0d0
+ RETURN
+ END SUBROUTINE energy_quad
+
+
+c!-------------------------------------------------------------------
+
+
+ SUBROUTINE eqn(Epol)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar, facd4, federmaus
+ alphapol1 = alphapol(itypi,itypj)
+c! R1 - distance between head of ith side chain and tail of jth sidechain
+ R1 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ END DO
+c! Pitagoras
+ R1 = dsqrt(R1)
+
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,1,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,1,itypi,itypj))**2))
+c--------------------------------------------------------------------
+c Polarization energy
+c Epol
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ RR1 = R1 * R1 / MomoFac1
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1)
+ epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
+c! epol = 0.0d0
+c!------------------------------------------------------------------
+c! derivative of Epol is Gpol...
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)
+ & / (fgb1 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1)
+ & * ( 2.0d0 - (0.5d0 * ee1) ) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))
+ & * (2.0d0 - 0.5d0 * ee1) )
+ & / (2.0d0 * fgb1)
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1
+c! dPOLdR1 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+c! dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Return the results
+c! (see comments in Eqq)
+ DO k = 1, 3
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ END DO
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
+ facd1 = d1 * vbld_inv(i+nres)
+ facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+
+ DO k = 1, 3
+ hawk = (erhead_tail(k,1) +
+ & facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dPOLdR1 * hawk
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dPOLdR1 * (erhead_tail(k,1)
+ & -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dPOLdR1 * erhead_tail(k,1)
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dPOLdR1 * erhead_tail(k,1)
+
+ END DO
+ RETURN
+ END SUBROUTINE eqn
+
+
+c!-------------------------------------------------------------------
+
+
+
+ SUBROUTINE enq(Epol)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar, facd3, adler
+ alphapol2 = alphapol(itypj,itypi)
+c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R2 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+c! Pitagoras
+ R2 = dsqrt(R2)
+
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,1,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,1,itypi,itypj))**2))
+c------------------------------------------------------------------------
+c Polarization energy
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR2 = R2 * R2 / MomoFac2
+ ee2 = exp(-(RR2 / (4.0d0 * a12sq)))
+ fgb2 = sqrt(RR2 + a12sq * ee2)
+ epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
+c! epol = 0.0d0
+c!-------------------------------------------------------------------
+c! derivative of Epol is Gpol...
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)
+ & / (fgb2 ** 5.0d0)
+ dFGBdR2 = ( (R2 / MomoFac2)
+ & * ( 2.0d0 - (0.5d0 * ee2) ) )
+ & / (2.0d0 * fgb2)
+ dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))
+ & * (2.0d0 - 0.5d0 * ee2) )
+ & / (2.0d0 * fgb2)
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2
+c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Return the results
+c! (See comments in Eqq)
+ DO k = 1, 3
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd2 = d2 * vbld_inv(j+nres)
+ facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+ DO k = 1, 3
+ condor = (erhead_tail(k,2)
+ & + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
+
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dPOLdR2 * (erhead_tail(k,2)
+ & -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dPOLdR2 * condor
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dPOLdR2 * erhead_tail(k,2)
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dPOLdR2 * erhead_tail(k,2)
+
+ END DO
+ RETURN
+ END SUBROUTINE enq
+
+
+c!-------------------------------------------------------------------
+
+
+ SUBROUTINE eqd(Ecl,Elj,Epol)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar, facd4, federmaus
+ alphapol1 = alphapol(itypi,itypj)
+ w1 = wqdip(1,itypi,itypj)
+ w2 = wqdip(2,itypi,itypj)
+ pis = sig0head(itypi,itypj)
+ eps_head = epshead(itypi,itypj)
+c!-------------------------------------------------------------------
+c! R1 - distance between head of ith side chain and tail of jth sidechain
+ R1 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ END DO
+c! Pitagoras
+ R1 = dsqrt(R1)
+
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,1,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,1,itypi,itypj))**2))
+
+c!-------------------------------------------------------------------
+c! ecl
+ sparrow = w1 * Qi * om1
+ hawk = w2 * Qi * Qi * (1.0d0 - sqom2)
+ Ecl = sparrow / Rhead**2.0d0
+ & - hawk / Rhead**4.0d0
+c!-------------------------------------------------------------------
+c! derivative of ecl is Gcl
+c! dF/dr part
+ dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0
+ & + 4.0d0 * hawk / Rhead**5.0d0
+c! dF/dom1
+ dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+c! dF/dom2
+ dGCLdOM2 = (2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+c--------------------------------------------------------------------
+c Polarization energy
+c Epol
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ RR1 = R1 * R1 / MomoFac1
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1)
+ epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
+c! epol = 0.0d0
+c!------------------------------------------------------------------
+c! derivative of Epol is Gpol...
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)
+ & / (fgb1 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1)
+ & * ( 2.0d0 - (0.5d0 * ee1) ) )
+ & / ( 2.0d0 * fgb1 )
+ dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))
+ & * (2.0d0 - 0.5d0 * ee1) )
+ & / (2.0d0 * fgb1)
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1
+c! dPOLdR1 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+c! dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Elj
+ pom = (pis / Rhead)**6.0d0
+ Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+c! derivative of Elj is Glj
+ dGLJdR = 4.0d0 * eps_head
+ & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))
+ & + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+c!-------------------------------------------------------------------
+c! Return the results
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ END DO
+
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres))
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres)
+
+ DO k = 1, 3
+ hawk = (erhead_tail(k,1) +
+ & facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dGCLdR * pom
+ & - dPOLdR1 * hawk
+ & - dGLJdR * pom
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dGCLdR * pom
+ & + dPOLdR1 * (erhead_tail(k,1)
+ & -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
+ & + dGLJdR * pom
+
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dGCLdR * erhead(k)
+ & - dPOLdR1 * erhead_tail(k,1)
+ & - dGLJdR * erhead(k)
+
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dGCLdR * erhead(k)
+ & + dPOLdR1 * erhead_tail(k,1)
+ & + dGLJdR * erhead(k)
+
+ END DO
+ RETURN
+ END SUBROUTINE eqd
+
+
+c!-------------------------------------------------------------------
+
+
+ SUBROUTINE edq(Ecl,Elj,Epol)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar, facd3, adler
+ alphapol2 = alphapol(itypj,itypi)
+ w1 = wqdip(1,itypi,itypj)
+ w2 = wqdip(2,itypi,itypj)
+ pis = sig0head(itypi,itypj)
+ eps_head = epshead(itypi,itypj)
+c!-------------------------------------------------------------------
+c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R2 = 0.0d0
+ DO k = 1, 3
+c! Calculate head-to-tail distances
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+c! Pitagoras
+ R2 = dsqrt(R2)
+
+c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+c! & +dhead(1,1,itypi,itypj))**2))
+c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+c! & +dhead(2,1,itypi,itypj))**2))
+
+
+c!-------------------------------------------------------------------
+c! ecl
+ sparrow = w1 * Qi * om1
+ hawk = w2 * Qi * Qi * (1.0d0 - sqom2)
+ ECL = sparrow / Rhead**2.0d0
+ & - hawk / Rhead**4.0d0
+c!-------------------------------------------------------------------
+c! derivative of ecl is Gcl
+c! dF/dr part
+ dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0
+ & + 4.0d0 * hawk / Rhead**5.0d0
+c! dF/dom1
+ dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+c! dF/dom2
+ dGCLdOM2 = (2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+c--------------------------------------------------------------------
+c Polarization energy
+c Epol
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR2 = R2 * R2 / MomoFac2
+ ee2 = exp(-(RR2 / (4.0d0 * a12sq)))
+ fgb2 = sqrt(RR2 + a12sq * ee2)
+ epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
+c! epol = 0.0d0
+c! derivative of Epol is Gpol...
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)
+ & / (fgb2 ** 5.0d0)
+ dFGBdR2 = ( (R2 / MomoFac2)
+ & * ( 2.0d0 - (0.5d0 * ee2) ) )
+ & / (2.0d0 * fgb2)
+ dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))
+ & * (2.0d0 - 0.5d0 * ee2) )
+ & / (2.0d0 * fgb2)
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2
+c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+c!-------------------------------------------------------------------
+c! Elj
+ pom = (pis / Rhead)**6.0d0
+ Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+c! derivative of Elj is Glj
+ dGLJdR = 4.0d0 * eps_head
+ & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))
+ & + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+c!-------------------------------------------------------------------
+c! Return the results
+c! (see comments in Eqq)
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j+nres) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ facd3 = dtail(1,itypi,itypj) * vbld_inv(i+nres)
+
+ DO k = 1, 3
+ condor = (erhead_tail(k,2)
+ & + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dGCLdR * pom
+ & - dPOLdR2 * (erhead_tail(k,2)
+ & -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
+ & - dGLJdR * pom
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dGCLdR * pom
+ & + dPOLdR2 * condor
+ & + dGLJdR * pom
+
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dGCLdR * erhead(k)
+ & - dPOLdR2 * erhead_tail(k,2)
+ & - dGLJdR * erhead(k)
+
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dGCLdR * erhead(k)
+ & + dPOLdR2 * erhead_tail(k,2)
+ & + dGLJdR * erhead(k)
+
+ END DO
+ RETURN
+ END SUBROUTINE edq
+
+
+C--------------------------------------------------------------------
+
+
+ SUBROUTINE edd(ECL)
+ IMPLICIT NONE
+ INCLUDE 'DIMENSIONS'
+ INCLUDE 'DIMENSIONS.ZSCOPT'
+ INCLUDE 'COMMON.CALC'
+ INCLUDE 'COMMON.CHAIN'
+ INCLUDE 'COMMON.CONTROL'
+ INCLUDE 'COMMON.DERIV'
+ INCLUDE 'COMMON.EMP'
+ INCLUDE 'COMMON.GEO'
+ INCLUDE 'COMMON.INTERACT'
+ INCLUDE 'COMMON.IOUNITS'
+ INCLUDE 'COMMON.LOCAL'
+ INCLUDE 'COMMON.NAMES'
+ INCLUDE 'COMMON.VAR'
+ double precision scalar
+c! csig = sigiso(itypi,itypj)
+ w1 = wqdip(1,itypi,itypj)
+ w2 = wqdip(2,itypi,itypj)
+c!-------------------------------------------------------------------
+c! ECL
+ fac = (om12 - 3.0d0 * om1 * om2)
+ c1 = (w1 / (Rhead**3.0d0)) * fac
+ c2 = (w2 / Rhead ** 6.0d0)
+ & * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+ ECL = c1 - c2
+c! write (*,*) "w1 = ", w1
+c! write (*,*) "w2 = ", w2
+c! write (*,*) "om1 = ", om1
+c! write (*,*) "om2 = ", om2
+c! write (*,*) "om12 = ", om12
+c! write (*,*) "fac = ", fac
+c! write (*,*) "c1 = ", c1
+c! write (*,*) "c2 = ", c2
+c! write (*,*) "Ecl = ", Ecl
+c! write (*,*) "c2_1 = ", (w2 / Rhead ** 6.0d0)
+c! write (*,*) "c2_2 = ",
+c! & (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+c!-------------------------------------------------------------------
+c! dervative of ECL is GCL...
+c! dECL/dr
+ c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0)
+ & * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+ dGCLdR = c1 - c2
+c! dECL/dom1
+ c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead**6.0d0)
+ & * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+ dGCLdOM1 = c1 - c2
+c! dECL/dom2
+ c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead**6.0d0)
+ & * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+ dGCLdOM2 = c1 - c2
+c! dECL/dom12
+ c1 = w1 / (Rhead ** 3.0d0)
+ c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0
+ dGCLdOM12 = c1 - c2
+c!-------------------------------------------------------------------
+c! Return the results
+c! (see comments in Eqq)
+ DO k= 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ DO k = 1, 3
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gvdwx(k,i) = gvdwx(k,i)
+ & - dGCLdR * pom
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+ gvdwx(k,j) = gvdwx(k,j)
+ & + dGCLdR * pom
+
+ gvdwc(k,i) = gvdwc(k,i)
+ & - dGCLdR * erhead(k)
+ gvdwc(k,j) = gvdwc(k,j)
+ & + dGCLdR * erhead(k)
+ END DO
+ RETURN
+ END SUBROUTINE edd
+
+
+c!-------------------------------------------------------------------
+
+
+ SUBROUTINE elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+ IMPLICIT NONE
+c! maxres
+ INCLUDE 'DIMENSIONS'
+c! itypi, itypj, i, j, k, l, chead,
+ INCLUDE 'COMMON.CALC'
+c! c, nres, dc_norm
+ INCLUDE 'COMMON.CHAIN'
+c! gradc, gradx
+ INCLUDE 'COMMON.DERIV'
+c! electrostatic gradients-specific variables
+ INCLUDE 'COMMON.EMP'
+c! wquad, dhead, alphiso, alphasur, rborn, epsintab
+ INCLUDE 'COMMON.INTERACT'
+c! io for debug, disable it in final builds
+ INCLUDE 'COMMON.IOUNITS'
+c!-------------------------------------------------------------------
+c! Variable Init
+
+c! what amino acid is the aminoacid j'th?
+ itypj = itype(j)
+c! 1/(Gas Constant * Thermostate temperature) = BetaT
+c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
+ BetaT = 1.0d0 / (298 * 1.987d-3)
+c! Gay-berne var's
+ sig0ij = sigma( itypi,itypj )
+ chi1 = chi( itypi, itypj )
+ chi2 = chi( itypj, itypi )
+ chi12 = chi1 * chi2
+ chip1 = chipp( itypi, itypj )
+ chip2 = chipp( itypj, itypi )
+ chip12 = chip1 * chip2
+c! write (2,*) "elgrad types",itypi,itypj,
+c! & " chi1",chi1," chi2",chi2," chi12",chi12,
+c! & " chip1",chip1," chip2",chip2," chip12",chip12
+c! not used by momo potential, but needed by sc_angular which is shared
+c! by all energy_potential subroutines
+ alf1 = 0.0d0
+ alf2 = 0.0d0
+ alf12 = 0.0d0
+c! location, location, location
+ xj = c( 1, nres+j ) - xi
+ yj = c( 2, nres+j ) - yi
+ zj = c( 3, nres+j ) - zi
+ dxj = dc_norm( 1, nres+j )
+ dyj = dc_norm( 2, nres+j )
+ dzj = dc_norm( 3, nres+j )
+c! distance from center of chain(?) to polar/charged head
+c! write (*,*) "istate = ", 1
+c! write (*,*) "ii = ", 1
+c! write (*,*) "jj = ", 1
+ d1 = dhead(1, 1, itypi, itypj)
+ d2 = dhead(2, 1, itypi, itypj)
+c! ai*aj from Fgb
+ a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
+c! a12sq = a12sq * a12sq
+c! charge of amino acid itypi is...
+ Qi = icharge(itypi)
+ Qj = icharge(itypj)
+ Qij = Qi * Qj
+c! chis1,2,12
+ chis1 = chis(itypi,itypj)
+ chis2 = chis(itypj,itypi)
+ chis12 = chis1 * chis2
+ sig1 = sigmap1(itypi,itypj)
+ sig2 = sigmap2(itypi,itypj)
+c! write (*,*) "sig1 = ", sig1
+c! write (*,*) "sig2 = ", sig2
+c! alpha factors from Fcav/Gcav
+ b1 = alphasur(1,itypi,itypj)
+ b2 = alphasur(2,itypi,itypj)
+ b3 = alphasur(3,itypi,itypj)
+ b4 = alphasur(4,itypi,itypj)
+c! used to determine whether we want to do quadrupole calculations
+ wqd = wquad(itypi, itypj)
+c! used by Fgb
+ eps_in = epsintab(itypi,itypj)
+ eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+c! write (*,*) "eps_inout_fac = ", eps_inout_fac
+c!-------------------------------------------------------------------
+c! tail location and distance calculations
+ Rtail = 0.0d0
+ DO k = 1, 3
+ ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i)
+ ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j)
+ END DO
+c! tail distances will be themselves usefull elswhere
+c1 (in Gcav, for example)
+ Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
+ Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
+ Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+ Rtail = dsqrt(
+ & (Rtail_distance(1)*Rtail_distance(1))
+ & + (Rtail_distance(2)*Rtail_distance(2))
+ & + (Rtail_distance(3)*Rtail_distance(3)))
+c!-------------------------------------------------------------------
+c! Calculate location and distance between polar heads
+c! distance between heads
+c! for each one of our three dimensional space...
+ DO k = 1,3
+c! location of polar head is computed by taking hydrophobic centre
+c! and moving by a d1 * dc_norm vector
+c! see unres publications for very informative images
+ chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+ chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres)
+c! distance
+c! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+c! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ Rhead_distance(k) = chead(k,2) - chead(k,1)
+ END DO
+c! pitagoras (root of sum of squares)
+ Rhead = dsqrt(
+ & (Rhead_distance(1)*Rhead_distance(1))
+ & + (Rhead_distance(2)*Rhead_distance(2))
+ & + (Rhead_distance(3)*Rhead_distance(3)))
+c!-------------------------------------------------------------------
+c! zero everything that should be zero'ed
+ Egb = 0.0d0
+ ECL = 0.0d0
+ Elj = 0.0d0
+ Equad = 0.0d0
+ Epol = 0.0d0
+ eheadtail = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ RETURN
+ END SUBROUTINE elgrad_init
+c!-------------------------------------------------------------------
+ subroutine sc_angular
+C Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
+C om12. Called by ebp, egb, and egbv.
+ implicit none
+ include 'COMMON.CALC'
+ include 'COMMON.IOUNITS'
+ erij(1)=xj*rij
+ erij(2)=yj*rij
+ erij(3)=zj*rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+c! om1 = 0.0d0
+c! om2 = 0.0d0
+c! om12 = 0.0d0
+ chiom12=chi12*om12
+C Calculate eps1(om12) and its derivative in om12
+ faceps1=1.0D0-om12*chiom12
+ faceps1_inv=1.0D0/faceps1
+ eps1=dsqrt(faceps1_inv)
+c write (2,*) "chi1",chi1," chi2",chi2," chi12",chi12
+c write (2,*) "fsceps1",faceps1," faceps1_inv",faceps1_inv,
+c & " eps1",eps1
+C Following variable is eps1*deps1/dom12
+ eps1_om12=faceps1_inv*chiom12
+c diagnostics only
+c faceps1_inv=om12
+c eps1=om12
+c eps1_om12=1.0d0
+c write (iout,*) "om12",om12," eps1",eps1
+C Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
+C and om12.
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
+ sigsq=1.0D0-facsig*faceps1_inv
+c write (2,*) "om1",om1," om2",om2," om1om2",om1om2,
+c & " chiom1",chiom1,
+c & " chiom2",chiom2," facsig",facsig," sigsq",sigsq
+ sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
+ sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
+ sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
+c diagnostics only
+c sigsq=1.0d0
+c sigsq_om1=0.0d0
+c sigsq_om2=0.0d0
+c sigsq_om12=0.0d0
+c write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
+c write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
+c & " eps1",eps1
+C Calculate eps2 and its derivatives in om1, om2, and om12.
+ chipom1=chip1*om1
+ chipom2=chip2*om2
+ chipom12=chip12*om12
+ facp=1.0D0-om12*chipom12
+ facp_inv=1.0D0/facp
+ facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
+c write (iout,*) "chipom1",chipom1," chipom2",chipom2,
+c & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
+C Following variable is the square root of eps2
+ eps2rt=1.0D0-facp1*facp_inv
+C Following three variables are the derivatives of the square root of eps
+C in om1, om2, and om12.
+ eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
+ eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
+ eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
+C Evaluate the "asymmetric" factor in the VDW constant, eps3
+c! Note that THIS is 0 in emomo, so we should probably move it out of sc_angular
+c! Or frankly, we should restructurize the whole energy section
+ eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
+c write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
+c write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
+c & " eps2rt_om12",eps2rt_om12
+C Calculate whole angle-dependent part of epsilon and contributions
+C to its derivatives
+ return
+ end
+C----------------------------------------------------------------------------
+ subroutine sc_grad
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.CALC'
+ double precision dcosom1(3),dcosom2(3)
+ eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
+ eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
+ eom12=evdwij*eps1_om12+eps2der*eps2rt_om12
+ & -2.0D0*alf12*eps3der+sigder*sigsq_om12
+ do k=1,3
+ dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
+ dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
+ enddo
+ do k=1,3
+ gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+ enddo
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ & +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
+ & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ & +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
+ & +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+ enddo
+C
+C Calculate the components of the gradient in DC and X
+C
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine vec_and_deriv
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ dimension uyder(3,3,2),uzder(3,3,2),vbld_inv_temp(2)
+C Compute the local reference systems. For reference system (i), the
+C X-axis points from CA(i) to CA(i+1), the Y axis is in the
+C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
+ do i=1,nres-1
+c if (i.eq.nres-1 .or. itel(i+1).eq.0) then
+ if (i.eq.nres-1) then
+C Case of the last full residue
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
+ costh=dcos(pi-theta(nres))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i-1)
+ uzder(3,1,1)= dc_norm(2,i-1)
+ uzder(1,2,1)= dc_norm(3,i-1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i-1)
+ uzder(1,3,1)=-dc_norm(2,i-1)
+ uzder(2,3,1)= dc_norm(1,i-1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+ endif
+C Compute the Y-axis
+ facy=fac
+ do k=1,3
+ uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i-1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+ uyder(j,j,1)=uyder(j,j,1)-costh
+ uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ else
+C Other residues
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
+ costh=dcos(pi-theta(i+2))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i+1)
+ uzder(3,1,1)= dc_norm(2,i+1)
+ uzder(1,2,1)= dc_norm(3,i+1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i+1)
+ uzder(1,3,1)=-dc_norm(2,i+1)
+ uzder(2,3,1)= dc_norm(1,i+1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+ endif
+C Compute the Y-axis
+ facy=fac
+ do k=1,3
+ uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i+1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+ uyder(j,j,1)=uyder(j,j,1)-costh
+ uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ endif
+ enddo
+ if (calc_grad) then
+ do i=1,nres-1
+ vbld_inv_temp(1)=vbld_inv(i+1)
+ if (i.lt.nres-1) then
+ vbld_inv_temp(2)=vbld_inv(i+2)
+ else
+ vbld_inv_temp(2)=vbld_inv(i)
+ endif
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=vbld_inv_temp(j)*uygrad(l,k,j,i)
+ uzgrad(l,k,j,i)=vbld_inv_temp(j)*uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine vec_and_deriv_test
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ dimension uyder(3,3,2),uzder(3,3,2)
+C Compute the local reference systems. For reference system (i), the
+C X-axis points from CA(i) to CA(i+1), the Y axis is in the
+C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
+ do i=1,nres-1
+ if (i.eq.nres-1) then
+C Case of the last full residue
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
+ costh=dcos(pi-theta(nres))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+c write (iout,*) 'fac',fac,
+c & 1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i-1)
+ uzder(3,1,1)= dc_norm(2,i-1)
+ uzder(1,2,1)= dc_norm(3,i-1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i-1)
+ uzder(1,3,1)=-dc_norm(2,i-1)
+ uzder(2,3,1)= dc_norm(1,i-1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+C Compute the Y-axis
+ do k=1,3
+ uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
+ enddo
+ facy=fac
+ facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
+ & (scalar(dc_norm(1,i-1),dc_norm(1,i-1))**2-
+ & scalar(dc_norm(1,i),dc_norm(1,i-1))**2))
+ do k=1,3
+c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ uy(k,i)=
+c & facy*(
+ & dc_norm(k,i-1)*scalar(dc_norm(1,i),dc_norm(1,i))
+ & -scalar(dc_norm(1,i),dc_norm(1,i-1))*dc_norm(k,i)
+c & )
+ enddo
+c write (iout,*) 'facy',facy,
+c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ do k=1,3
+ uy(k,i)=facy*uy(k,i)
+ enddo
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i-1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+c uyder(j,j,1)=uyder(j,j,1)-costh
+c uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ uyder(j,j,1)=uyder(j,j,1)
+ & -scalar(dc_norm(1,i),dc_norm(1,i-1))
+ uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
+ & +uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ else
+C Other residues
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
+ costh=dcos(pi-theta(i+2))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i+1)
+ uzder(3,1,1)= dc_norm(2,i+1)
+ uzder(1,2,1)= dc_norm(3,i+1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i+1)
+ uzder(1,3,1)=-dc_norm(2,i+1)
+ uzder(2,3,1)= dc_norm(1,i+1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+C Compute the Y-axis
+ facy=fac
+ facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
+ & (scalar(dc_norm(1,i+1),dc_norm(1,i+1))**2-
+ & scalar(dc_norm(1,i),dc_norm(1,i+1))**2))
+ do k=1,3
+c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ uy(k,i)=
+c & facy*(
+ & dc_norm(k,i+1)*scalar(dc_norm(1,i),dc_norm(1,i))
+ & -scalar(dc_norm(1,i),dc_norm(1,i+1))*dc_norm(k,i)
+c & )
+ enddo
+c write (iout,*) 'facy',facy,
+c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ do k=1,3
+ uy(k,i)=facy*uy(k,i)
+ enddo
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i+1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+c uyder(j,j,1)=uyder(j,j,1)-costh
+c uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ uyder(j,j,1)=uyder(j,j,1)
+ & -scalar(dc_norm(1,i),dc_norm(1,i+1))
+ uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
+ & +uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ enddo
+ do i=1,nres-1
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i)
+ uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine check_vecgrad
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ dimension uygradt(3,3,2,maxres),uzgradt(3,3,2,maxres)
+ dimension uyt(3,maxres),uzt(3,maxres)
+ dimension uygradn(3,3,2),uzgradn(3,3,2),erij(3)
+ double precision delta /1.0d-7/
+ call vec_and_deriv
+cd do i=1,nres
+crc write(iout,'(2i5,2(3f10.5,5x))') i,1,dc_norm(:,i)
+crc write(iout,'(2i5,2(3f10.5,5x))') i,2,uy(:,i)
+crc write(iout,'(2i5,2(3f10.5,5x)/)')i,3,uz(:,i)
+cd write(iout,'(2i5,2(3f10.5,5x))') i,1,
+cd & (dc_norm(if90,i),if90=1,3)
+cd write(iout,'(2i5,2(3f10.5,5x))') i,2,(uy(if90,i),if90=1,3)
+cd write(iout,'(2i5,2(3f10.5,5x)/)')i,3,(uz(if90,i),if90=1,3)
+cd write(iout,'(a)')
+cd enddo
+ do i=1,nres
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygradt(l,k,j,i)=uygrad(l,k,j,i)
+ uzgradt(l,k,j,i)=uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ call vec_and_deriv
+ do i=1,nres
+ do j=1,3
+ uyt(j,i)=uy(j,i)
+ uzt(j,i)=uz(j,i)
+ enddo
+ enddo
+ do i=1,nres
+cd write (iout,*) 'i=',i
+ do k=1,3
+ erij(k)=dc_norm(k,i)
+ enddo
+ do j=1,3
+ do k=1,3
+ dc_norm(k,i)=erij(k)
+ enddo
+ dc_norm(j,i)=dc_norm(j,i)+delta
+c fac=dsqrt(scalar(dc_norm(1,i),dc_norm(1,i)))
+c do k=1,3
+c dc_norm(k,i)=dc_norm(k,i)/fac
+c enddo
+c write (iout,*) (dc_norm(k,i),k=1,3)
+c write (iout,*) (erij(k),k=1,3)
+ call vec_and_deriv
+ do k=1,3
+ uygradn(k,j,1)=(uy(k,i)-uyt(k,i))/delta
+ uygradn(k,j,2)=(uy(k,i-1)-uyt(k,i-1))/delta
+ uzgradn(k,j,1)=(uz(k,i)-uzt(k,i))/delta
+ uzgradn(k,j,2)=(uz(k,i-1)-uzt(k,i-1))/delta
+ enddo
+c write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+c & j,(uzgradt(k,j,1,i),k=1,3),(uzgradn(k,j,1),k=1,3),
+c & (uzgradt(k,j,2,i-1),k=1,3),(uzgradn(k,j,2),k=1,3)
+ enddo
+ do k=1,3
+ dc_norm(k,i)=erij(k)
+ enddo
+cd do k=1,3
+cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+cd & k,(uygradt(k,l,1,i),l=1,3),(uygradn(k,l,1),l=1,3),
+cd & (uygradt(k,l,2,i-1),l=1,3),(uygradn(k,l,2),l=1,3)
+cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+cd & k,(uzgradt(k,l,1,i),l=1,3),(uzgradn(k,l,1),l=1,3),
+cd & (uzgradt(k,l,2,i-1),l=1,3),(uzgradn(k,l,2),l=1,3)
+cd write (iout,'(a)')
+cd enddo
+ enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine set_matrices
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ double precision auxvec(2),auxmat(2,2)
+C
+C Compute the virtual-bond-torsional-angle dependent quantities needed
+C to calculate the el-loc multibody terms of various order.
+C
+#ifdef NEWCORR
+ do i=3,nres+1
+ if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ iti = itortyp(itype(i-2))
+ else
+ iti=ntortyp+1
+ endif
+ if (i.gt. nnt+1 .and. i.lt.nct+1) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+ b1(1,i-2)=bnew1(1,1,iti)*sin(theta(i-1)/2.0)
+ & +bnew1(2,1,iti)*sin(theta(i-1))
+ & +bnew1(3,1,iti)*cos(theta(i-1)/2.0)
+ b2(1,i-2)=bnew2(1,1,iti)*sin(theta(i-1)/2.0)
+ & +bnew2(2,1,iti)*sin(theta(i-1))
+ & +bnew2(3,1,iti)*cos(theta(i-1)/2.0)
+ b1(2,i-2)=bnew1(1,2,iti)
+ b2(2,i-2)=bnew2(1,2,iti)
+ EE(1,1,i-2)=eenew(1,iti)*dcos(theta(i-1))
+ EE(1,2,i-2)=eeold(1,2,iti)
+ EE(2,1,i-2)=eeold(2,1,iti)
+ EE(2,2,i-2)=eeold(2,2,iti)
+ b1tilde(1,i-2)=b1(1,i-2)
+ b1tilde(2,i-2)=-b1(2,i-2)
+ enddo
+#endif
+ do i=3,nres+1
+ if (i .lt. nres+1) then
+ sin1=dsin(phi(i))
+ cos1=dcos(phi(i))
+ sintab(i-2)=sin1
+ costab(i-2)=cos1
+ obrot(1,i-2)=cos1
+ obrot(2,i-2)=sin1
+ sin2=dsin(2*phi(i))
+ cos2=dcos(2*phi(i))
+ sintab2(i-2)=sin2
+ costab2(i-2)=cos2
+ obrot2(1,i-2)=cos2
+ obrot2(2,i-2)=sin2
+ Ug(1,1,i-2)=-cos1
+ Ug(1,2,i-2)=-sin1
+ Ug(2,1,i-2)=-sin1
+ Ug(2,2,i-2)= cos1
+ Ug2(1,1,i-2)=-cos2
+ Ug2(1,2,i-2)=-sin2
+ Ug2(2,1,i-2)=-sin2
+ Ug2(2,2,i-2)= cos2
+ else
+ costab(i-2)=1.0d0
+ sintab(i-2)=0.0d0
+ obrot(1,i-2)=1.0d0
+ obrot(2,i-2)=0.0d0
+ obrot2(1,i-2)=0.0d0
+ obrot2(2,i-2)=0.0d0
+ Ug(1,1,i-2)=1.0d0
+ Ug(1,2,i-2)=0.0d0
+ Ug(2,1,i-2)=0.0d0
+ Ug(2,2,i-2)=1.0d0
+ Ug2(1,1,i-2)=0.0d0
+ Ug2(1,2,i-2)=0.0d0
+ Ug2(2,1,i-2)=0.0d0
+ Ug2(2,2,i-2)=0.0d0
+ endif
+ if (i .gt. 3 .and. i .lt. nres+1) then
+ obrot_der(1,i-2)=-sin1
+ obrot_der(2,i-2)= cos1
+ Ugder(1,1,i-2)= sin1
+ Ugder(1,2,i-2)=-cos1
+ Ugder(2,1,i-2)=-cos1
+ Ugder(2,2,i-2)=-sin1
+ dwacos2=cos2+cos2
+ dwasin2=sin2+sin2
+ obrot2_der(1,i-2)=-dwasin2
+ obrot2_der(2,i-2)= dwacos2
+ Ug2der(1,1,i-2)= dwasin2
+ Ug2der(1,2,i-2)=-dwacos2
+ Ug2der(2,1,i-2)=-dwacos2
+ Ug2der(2,2,i-2)=-dwasin2
+ else
+ obrot_der(1,i-2)=0.0d0
+ obrot_der(2,i-2)=0.0d0
+ Ugder(1,1,i-2)=0.0d0
+ Ugder(1,2,i-2)=0.0d0
+ Ugder(2,1,i-2)=0.0d0
+ Ugder(2,2,i-2)=0.0d0
+ obrot2_der(1,i-2)=0.0d0
+ obrot2_der(2,i-2)=0.0d0
+ Ug2der(1,1,i-2)=0.0d0
+ Ug2der(1,2,i-2)=0.0d0
+ Ug2der(2,1,i-2)=0.0d0
+ Ug2der(2,2,i-2)=0.0d0
+ endif
+ if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
+ iti = itortyp(itype(i-2))
+ else
+ iti=ntortyp+1
+ endif
+ if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+cd write (iout,*) '*******i',i,' iti1',iti
+cd write (iout,*) 'b1',b1(:,iti)
+cd write (iout,*) 'b2',b2(:,iti)
+cd write (iout,*) 'Ug',Ug(:,:,i-2)
+ if (i .gt. iatel_s+2) then
+ call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2))
+ call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2))
+ call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2))
+ call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2))
+ call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2))
+ call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2))
+ call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2))
+ else
+ do k=1,2
+ Ub2(k,i-2)=0.0d0
+ Ctobr(k,i-2)=0.0d0
+ Dtobr2(k,i-2)=0.0d0
+ do l=1,2
+ EUg(l,k,i-2)=0.0d0
+ CUg(l,k,i-2)=0.0d0
+ DUg(l,k,i-2)=0.0d0
+ DtUg2(l,k,i-2)=0.0d0
+ enddo
+ enddo
+ endif
+ call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2))
+ call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2))
+ call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2))
+ call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2))
+ call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
+ call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2))
+ call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2))
+ do k=1,2
+ muder(k,i-2)=Ub2der(k,i-2)
+ enddo
+ if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+ do k=1,2
+ mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
+ enddo
+C Vectors and matrices dependent on a single virtual-bond dihedral.
+ call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
+ call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
+ call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2))
+ call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2))
+ call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2))
+ call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2))
+ call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2))
+cd write (iout,*) 'i',i,' mu ',(mu(k,i-2),k=1,2),
+cd & ' mu1',(b1(k,i-2),k=1,2),' mu2',(Ub2(k,i-2),k=1,2)
+ enddo
+C Matrices dependent on two consecutive virtual-bond dihedrals.
+C The order of matrices is from left to right.
+ do i=2,nres-1
+ call matmat2(DtUg2(1,1,i-1),EUg(1,1,i),DtUg2EUg(1,1,i))
+ call matmat2(DtUg2der(1,1,i-1),EUg(1,1,i),DtUg2EUgder(1,1,1,i))
+ call matmat2(DtUg2(1,1,i-1),EUgder(1,1,i),DtUg2EUgder(1,1,2,i))
+ call transpose2(DtUg2(1,1,i-1),auxmat(1,1))
+ call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUg(1,1,i))
+ call matmat2(auxmat(1,1),EUgder(1,1,i),Ug2DtEUgder(1,1,2,i))
+ call transpose2(DtUg2der(1,1,i-1),auxmat(1,1))
+ call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i))
+ enddo
+cd do i=1,nres
+cd iti = itortyp(itype(i))
+cd write (iout,*) i
+cd do j=1,2
+cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
+cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
+cd enddo
+cd enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
+C
+C This subroutine calculates the average interaction energy and its gradient
+C in the virtual-bond vectors between non-adjacent peptide groups, based on
+C the potential described in Liwo et al., Protein Sci., 1993, 2, 1715.
+C The potential depends both on the distance of peptide-group centers and on
+C the orientation of the CA-CA virtual bonds.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
+ & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
+ double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1
+c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
+ double precision scal_el /0.5d0/
+C 12/13/98
+C 13-go grudnia roku pamietnego...
+ double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
+ & 0.0d0,1.0d0,0.0d0,
+ & 0.0d0,0.0d0,1.0d0/
+cd write(iout,*) 'In EELEC'
+cd do i=1,nloctyp
+cd write(iout,*) 'Type',i
+cd write(iout,*) 'B1',B1(:,i)
+cd write(iout,*) 'B2',B2(:,i)
+cd write(iout,*) 'CC',CC(:,:,i)
+cd write(iout,*) 'DD',DD(:,:,i)
+cd write(iout,*) 'EE',EE(:,:,i)
+cd enddo
+cd call check_vecgrad
+cd stop
+ if (icheckgrad.eq.1) then
+ do i=1,nres-1
+ fac=1.0d0/dsqrt(scalar(dc(1,i),dc(1,i)))
+ do k=1,3
+ dc_norm(k,i)=dc(k,i)*fac
+ enddo
+c write (iout,*) 'i',i,' fac',fac
+ enddo
+ endif
+ if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
+ & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or.
+ & wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then
+cd if (wel_loc.gt.0.0d0) then
+ if (icheckgrad.eq.1) then
+ call vec_and_deriv_test
+ else
+ call vec_and_deriv
+ endif
+ call set_matrices
+ endif
+cd do i=1,nres-1
+cd write (iout,*) 'i=',i
+cd do k=1,3
+cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i)
+cd enddo
+cd do k=1,3
+cd write (iout,'(f10.5,2x,3f10.5,2x,3f10.5)')
+cd & uz(k,i),(uzgrad(k,l,1,i),l=1,3),(uzgrad(k,l,2,i),l=1,3)
+cd enddo
+cd enddo
+ num_conti_hb=0
+ ees=0.0D0
+ evdw1=0.0D0
+ eel_loc=0.0d0
+ eello_turn3=0.0d0
+ eello_turn4=0.0d0
+ ind=0
+ do i=1,nres
+ num_cont_hb(i)=0
+ enddo
+cd print '(a)','Enter EELEC'
+cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
+ do i=1,nres
+ gel_loc_loc(i)=0.0d0
+ gcorr_loc(i)=0.0d0
+ enddo
+ do i=iatel_s,iatel_e
+ if (itel(i).eq.0) goto 1215
+ dxi=dc(1,i)
+ dyi=dc(2,i)
+ dzi=dc(3,i)
+ dx_normi=dc_norm(1,i)
+ dy_normi=dc_norm(2,i)
+ dz_normi=dc_norm(3,i)
+ xmedi=c(1,i)+0.5d0*dxi
+ ymedi=c(2,i)+0.5d0*dyi
+ zmedi=c(3,i)+0.5d0*dzi
+ num_conti=0
+c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
+ do j=ielstart(i),ielend(i)
+ if (itel(j).eq.0) goto 1216
+ ind=ind+1
+ iteli=itel(i)
+ itelj=itel(j)
+ if (j.eq.i+2 .and. itelj.eq.2) iteli=2
+ aaa=app(iteli,itelj)
+ bbb=bpp(iteli,itelj)
+C Diagnostics only!!!
+c aaa=0.0D0
+c bbb=0.0D0
+c ael6i=0.0D0
+c ael3i=0.0D0
+C End diagnostics
+ ael6i=ael6(iteli,itelj)
+ ael3i=ael3(iteli,itelj)
+ dxj=dc(1,j)
+ dyj=dc(2,j)
+ dzj=dc(3,j)
+ dx_normj=dc_norm(1,j)
+ dy_normj=dc_norm(2,j)
+ dz_normj=dc_norm(3,j)
+ xj=c(1,j)+0.5D0*dxj-xmedi
+ yj=c(2,j)+0.5D0*dyj-ymedi
+ zj=c(3,j)+0.5D0*dzj-zmedi
+ rij=xj*xj+yj*yj+zj*zj
+ rrmij=1.0D0/rij
+ rij=dsqrt(rij)
+ rmij=1.0D0/rij
+ r3ij=rrmij*rmij
+ r6ij=r3ij*r3ij
+ cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj
+ cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij
+ cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij
+ fac=cosa-3.0D0*cosb*cosg
+ ev1=aaa*r6ij*r6ij
+c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions
+ if (j.eq.i+2) ev1=scal_el*ev1
+ ev2=bbb*r6ij
+ fac3=ael6i*r6ij
+ fac4=ael3i*r3ij
+ evdwij=ev1+ev2
+ el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
+ el2=fac4*fac
+ eesij=el1+el2
+c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij
+C 12/26/95 - for the evaluation of multi-body H-bonding interactions
+ ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
+ ees=ees+eesij
+ evdw1=evdw1+evdwij
+cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
+cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
+cd & xmedi,ymedi,zmedi,xj,yj,zj
+C
+C Calculate contributions to the Cartesian gradient.
+C
+#ifdef SPLITELE
+ facvdw=-6*rrmij*(ev1+evdwij)
+ facel=-3*rrmij*(el1+eesij)
+ fac1=fac
+ erij(1)=xj*rmij
+ erij(2)=yj*rmij
+ erij(3)=zj*rmij
+ if (calc_grad) then
+*
+* Radial derivatives. First process both termini of the fragment (i,j)
+*
+ ggg(1)=facel*xj
+ ggg(2)=facel*yj
+ ggg(3)=facel*zj
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gelc(k,i)=gelc(k,i)+ghalf
+ gelc(k,j)=gelc(k,j)+ghalf
+ enddo
+*
+* Loop over residues i+1 thru j-1.
+*
+ do k=i+1,j-1
+ do l=1,3
+ gelc(l,k)=gelc(l,k)+ggg(l)
+ enddo
+ enddo
+ ggg(1)=facvdw*xj
+ ggg(2)=facvdw*yj
+ ggg(3)=facvdw*zj
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gvdwpp(k,i)=gvdwpp(k,i)+ghalf
+ gvdwpp(k,j)=gvdwpp(k,j)+ghalf
+ enddo
+*
+* Loop over residues i+1 thru j-1.
+*
+ do k=i+1,j-1
+ do l=1,3
+ gvdwpp(l,k)=gvdwpp(l,k)+ggg(l)
+ enddo
+ enddo
+#else
+ facvdw=ev1+evdwij
+ facel=el1+eesij
+ fac1=fac
+ fac=-3*rrmij*(facvdw+facvdw+facel)
+ erij(1)=xj*rmij
+ erij(2)=yj*rmij
+ erij(3)=zj*rmij
+ if (calc_grad) then
+*
+* Radial derivatives. First process both termini of the fragment (i,j)
+*
+ ggg(1)=fac*xj
+ ggg(2)=fac*yj
+ ggg(3)=fac*zj
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gelc(k,i)=gelc(k,i)+ghalf
+ gelc(k,j)=gelc(k,j)+ghalf
+ enddo
+*
+* Loop over residues i+1 thru j-1.
+*
+ do k=i+1,j-1
+ do l=1,3
+ gelc(l,k)=gelc(l,k)+ggg(l)
+ enddo
+ enddo
+#endif
+*
+* Angular part
+*
+ ecosa=2.0D0*fac3*fac1+fac4
+ fac4=-3.0D0*fac4
+ fac3=-6.0D0*fac3
+ ecosb=(fac3*(fac1*cosg+cosb)+cosg*fac4)
+ ecosg=(fac3*(fac1*cosb+cosg)+cosb*fac4)
+ do k=1,3
+ dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
+ dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
+ enddo
+cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
+cd & (dcosg(k),k=1,3)
+ do k=1,3
+ ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+ enddo
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gelc(k,i)=gelc(k,i)+ghalf
+ & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
+ & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ gelc(k,j)=gelc(k,j)+ghalf
+ & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
+ & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ enddo
+ do k=i+1,j-1
+ do l=1,3
+ gelc(l,k)=gelc(l,k)+ggg(l)
+ enddo
+ enddo
+ endif
+
+ IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
+ & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0
+ & .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
+C
+C 9/25/99 Mixed third-order local-electrostatic terms. The local-interaction
+C energy of a peptide unit is assumed in the form of a second-order
+C Fourier series in the angles lambda1 and lambda2 (see Nishikawa et al.
+C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms
+C are computed for EVERY pair of non-contiguous peptide groups.
+C
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ kkk=0
+ do k=1,2
+ do l=1,2
+ kkk=kkk+1
+ muij(kkk)=mu(k,i)*mu(l,j)
+ enddo
+ enddo
+cd write (iout,*) 'EELEC: i',i,' j',j
+cd write (iout,*) 'j',j,' j1',j1,' j2',j2
+cd write(iout,*) 'muij',muij
+ ury=scalar(uy(1,i),erij)
+ urz=scalar(uz(1,i),erij)
+ vry=scalar(uy(1,j),erij)
+ vrz=scalar(uz(1,j),erij)
+ a22=scalar(uy(1,i),uy(1,j))-3*ury*vry
+ a23=scalar(uy(1,i),uz(1,j))-3*ury*vrz
+ a32=scalar(uz(1,i),uy(1,j))-3*urz*vry
+ a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz
+C For diagnostics only
+cd a22=1.0d0
+cd a23=1.0d0
+cd a32=1.0d0
+cd a33=1.0d0
+ fac=dsqrt(-ael6i)*r3ij
+cd write (2,*) 'fac=',fac
+C For diagnostics only
+cd fac=1.0d0
+ a22=a22*fac
+ a23=a23*fac
+ a32=a32*fac
+ a33=a33*fac
+cd write (iout,'(4i5,4f10.5)')
+cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
+cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
+cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') (uy(k,i),k=1,3),
+cd & (uz(k,i),k=1,3),(uy(k,j),k=1,3),(uz(k,j),k=1,3)
+cd write (iout,'(4f10.5)')
+cd & scalar(uy(1,i),uy(1,j)),scalar(uy(1,i),uz(1,j)),
+cd & scalar(uz(1,i),uy(1,j)),scalar(uz(1,i),uz(1,j))
+cd write (iout,'(4f10.5)') ury,urz,vry,vrz
+cd write (iout,'(2i3,9f10.5/)') i,j,
+cd & fac22,a22,fac23,a23,fac32,a32,fac33,a33,eel_loc_ij
+ if (calc_grad) then
+C Derivatives of the elements of A in virtual-bond vectors
+ call unormderiv(erij(1),unmat(1,1),rmij,erder(1,1))
+cd do k=1,3
+cd do l=1,3
+cd erder(k,l)=0.0d0
+cd enddo
+cd enddo
+ do k=1,3
+ uryg(k,1)=scalar(erder(1,k),uy(1,i))
+ uryg(k,2)=scalar(uygrad(1,k,1,i),erij(1))
+ uryg(k,3)=scalar(uygrad(1,k,2,i),erij(1))
+ urzg(k,1)=scalar(erder(1,k),uz(1,i))
+ urzg(k,2)=scalar(uzgrad(1,k,1,i),erij(1))
+ urzg(k,3)=scalar(uzgrad(1,k,2,i),erij(1))
+ vryg(k,1)=scalar(erder(1,k),uy(1,j))
+ vryg(k,2)=scalar(uygrad(1,k,1,j),erij(1))
+ vryg(k,3)=scalar(uygrad(1,k,2,j),erij(1))
+ vrzg(k,1)=scalar(erder(1,k),uz(1,j))
+ vrzg(k,2)=scalar(uzgrad(1,k,1,j),erij(1))
+ vrzg(k,3)=scalar(uzgrad(1,k,2,j),erij(1))
+ enddo
+cd do k=1,3
+cd do l=1,3
+cd uryg(k,l)=0.0d0
+cd urzg(k,l)=0.0d0
+cd vryg(k,l)=0.0d0
+cd vrzg(k,l)=0.0d0
+cd enddo
+cd enddo
+C Compute radial contributions to the gradient
+ facr=-3.0d0*rrmij
+ a22der=a22*facr
+ a23der=a23*facr
+ a32der=a32*facr
+ a33der=a33*facr
+cd a22der=0.0d0
+cd a23der=0.0d0
+cd a32der=0.0d0
+cd a33der=0.0d0
+ agg(1,1)=a22der*xj
+ agg(2,1)=a22der*yj
+ agg(3,1)=a22der*zj
+ agg(1,2)=a23der*xj
+ agg(2,2)=a23der*yj
+ agg(3,2)=a23der*zj
+ agg(1,3)=a32der*xj
+ agg(2,3)=a32der*yj
+ agg(3,3)=a32der*zj
+ agg(1,4)=a33der*xj
+ agg(2,4)=a33der*yj
+ agg(3,4)=a33der*zj
+C Add the contributions coming from er
+ fac3=-3.0d0*fac
+ do k=1,3
+ agg(k,1)=agg(k,1)+fac3*(uryg(k,1)*vry+vryg(k,1)*ury)
+ agg(k,2)=agg(k,2)+fac3*(uryg(k,1)*vrz+vrzg(k,1)*ury)
+ agg(k,3)=agg(k,3)+fac3*(urzg(k,1)*vry+vryg(k,1)*urz)
+ agg(k,4)=agg(k,4)+fac3*(urzg(k,1)*vrz+vrzg(k,1)*urz)
+ enddo
+ do k=1,3
+C Derivatives in DC(i)
+ ghalf1=0.5d0*agg(k,1)
+ ghalf2=0.5d0*agg(k,2)
+ ghalf3=0.5d0*agg(k,3)
+ ghalf4=0.5d0*agg(k,4)
+ aggi(k,1)=fac*(scalar(uygrad(1,k,1,i),uy(1,j))
+ & -3.0d0*uryg(k,2)*vry)+ghalf1
+ aggi(k,2)=fac*(scalar(uygrad(1,k,1,i),uz(1,j))
+ & -3.0d0*uryg(k,2)*vrz)+ghalf2
+ aggi(k,3)=fac*(scalar(uzgrad(1,k,1,i),uy(1,j))
+ & -3.0d0*urzg(k,2)*vry)+ghalf3
+ aggi(k,4)=fac*(scalar(uzgrad(1,k,1,i),uz(1,j))
+ & -3.0d0*urzg(k,2)*vrz)+ghalf4
+C Derivatives in DC(i+1)
+ aggi1(k,1)=fac*(scalar(uygrad(1,k,2,i),uy(1,j))
+ & -3.0d0*uryg(k,3)*vry)+agg(k,1)
+ aggi1(k,2)=fac*(scalar(uygrad(1,k,2,i),uz(1,j))
+ & -3.0d0*uryg(k,3)*vrz)+agg(k,2)
+ aggi1(k,3)=fac*(scalar(uzgrad(1,k,2,i),uy(1,j))
+ & -3.0d0*urzg(k,3)*vry)+agg(k,3)
+ aggi1(k,4)=fac*(scalar(uzgrad(1,k,2,i),uz(1,j))
+ & -3.0d0*urzg(k,3)*vrz)+agg(k,4)
+C Derivatives in DC(j)
+ aggj(k,1)=fac*(scalar(uygrad(1,k,1,j),uy(1,i))
+ & -3.0d0*vryg(k,2)*ury)+ghalf1
+ aggj(k,2)=fac*(scalar(uzgrad(1,k,1,j),uy(1,i))
+ & -3.0d0*vrzg(k,2)*ury)+ghalf2
+ aggj(k,3)=fac*(scalar(uygrad(1,k,1,j),uz(1,i))
+ & -3.0d0*vryg(k,2)*urz)+ghalf3
+ aggj(k,4)=fac*(scalar(uzgrad(1,k,1,j),uz(1,i))
+ & -3.0d0*vrzg(k,2)*urz)+ghalf4
+C Derivatives in DC(j+1) or DC(nres-1)
+ aggj1(k,1)=fac*(scalar(uygrad(1,k,2,j),uy(1,i))
+ & -3.0d0*vryg(k,3)*ury)
+ aggj1(k,2)=fac*(scalar(uzgrad(1,k,2,j),uy(1,i))
+ & -3.0d0*vrzg(k,3)*ury)
+ aggj1(k,3)=fac*(scalar(uygrad(1,k,2,j),uz(1,i))
+ & -3.0d0*vryg(k,3)*urz)
+ aggj1(k,4)=fac*(scalar(uzgrad(1,k,2,j),uz(1,i))
+ & -3.0d0*vrzg(k,3)*urz)
+cd aggi(k,1)=ghalf1
+cd aggi(k,2)=ghalf2
+cd aggi(k,3)=ghalf3
+cd aggi(k,4)=ghalf4
+C Derivatives in DC(i+1)
+cd aggi1(k,1)=agg(k,1)
+cd aggi1(k,2)=agg(k,2)
+cd aggi1(k,3)=agg(k,3)
+cd aggi1(k,4)=agg(k,4)
+C Derivatives in DC(j)
+cd aggj(k,1)=ghalf1
+cd aggj(k,2)=ghalf2
+cd aggj(k,3)=ghalf3
+cd aggj(k,4)=ghalf4
+C Derivatives in DC(j+1)
+cd aggj1(k,1)=0.0d0
+cd aggj1(k,2)=0.0d0
+cd aggj1(k,3)=0.0d0
+cd aggj1(k,4)=0.0d0
+ if (j.eq.nres-1 .and. i.lt.j-2) then
+ do l=1,4
+ aggj1(k,l)=aggj1(k,l)+agg(k,l)
+cd aggj1(k,l)=agg(k,l)
+ enddo
+ endif
+ enddo
+ endif
+c goto 11111
+C Check the loc-el terms by numerical integration
+ acipa(1,1)=a22
+ acipa(1,2)=a23
+ acipa(2,1)=a32
+ acipa(2,2)=a33
+ a22=-a22
+ a23=-a23
+ do l=1,2
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ if (j.lt.nres-1) then
+ a22=-a22
+ a32=-a32
+ do l=1,3,2
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ else
+ a22=-a22
+ a23=-a23
+ a32=-a32
+ a33=-a33
+ do l=1,4
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ endif
+ ENDIF ! WCORR
+11111 continue
+ IF (wel_loc.gt.0.0d0) THEN
+C Contribution to the local-electrostatic energy coming from the i-j pair
+ eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
+ & +a33*muij(4)
+cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
+cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
+ eel_loc=eel_loc+eel_loc_ij
+C Partial derivatives in virtual-bond dihedral angles gamma
+ if (calc_grad) then
+ if (i.gt.1)
+ & gel_loc_loc(i-1)=gel_loc_loc(i-1)+
+ & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
+ & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)
+ gel_loc_loc(j-1)=gel_loc_loc(j-1)+
+ & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
+ & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)
+cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij)
+cd write(iout,*) 'agg ',agg
+cd write(iout,*) 'aggi ',aggi
+cd write(iout,*) 'aggi1',aggi1
+cd write(iout,*) 'aggj ',aggj
+cd write(iout,*) 'aggj1',aggj1
+
+C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
+ do l=1,3
+ ggg(l)=agg(l,1)*muij(1)+
+ & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)
+ enddo
+ do k=i+2,j2
+ do l=1,3
+ gel_loc(l,k)=gel_loc(l,k)+ggg(l)
+ enddo
+ enddo
+C Remaining derivatives of eello
+ do l=1,3
+ gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
+ gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
+ gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
+ gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
+ enddo
+ endif
+ ENDIF
+ if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
+C Contributions from turns
+ a_temp(1,1)=a22
+ a_temp(1,2)=a23
+ a_temp(2,1)=a32
+ a_temp(2,2)=a33
+ call eturn34(i,j,eello_turn3,eello_turn4)
+ endif
+C Change 12/26/95 to calculate four-body contributions to H-bonding energy
+ if (j.gt.i+1 .and. num_conti.le.maxconts) then
+C
+C Calculate the contact function. The ith column of the array JCONT will
+C contain the numbers of atoms that make contacts with the atom I (of numbers
+C greater than I). The arrays FACONT and GACONT will contain the values of
+C the contact function and its derivative.
+c r0ij=1.02D0*rpp(iteli,itelj)
+c r0ij=1.11D0*rpp(iteli,itelj)
+ r0ij=2.20D0*rpp(iteli,itelj)
+c r0ij=1.55D0*rpp(iteli,itelj)
+ call gcont(rij,r0ij,1.0D0,0.2d0*r0ij,fcont,fprimcont)
+ if (fcont.gt.0.0D0) then
+ num_conti=num_conti+1
+ if (num_conti.gt.maxconts) then
+ write (iout,*) 'WARNING - max. # of contacts exceeded;',
+ & ' will skip next contacts for this conf.'
+ else
+ jcont_hb(num_conti,i)=j
+ IF (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.
+ & wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
+C 9/30/99 (AL) - store components necessary to evaluate higher-order loc-el
+C terms.
+ d_cont(num_conti,i)=rij
+cd write (2,'(3e15.5)') rij,r0ij+0.2d0*r0ij,rij
+C --- Electrostatic-interaction matrix ---
+ a_chuj(1,1,num_conti,i)=a22
+ a_chuj(1,2,num_conti,i)=a23
+ a_chuj(2,1,num_conti,i)=a32
+ a_chuj(2,2,num_conti,i)=a33
+C --- Gradient of rij
+ do kkk=1,3
+ grij_hb_cont(kkk,num_conti,i)=erij(kkk)
+ enddo
+c if (i.eq.1) then
+c a_chuj(1,1,num_conti,i)=-0.61d0
+c a_chuj(1,2,num_conti,i)= 0.4d0
+c a_chuj(2,1,num_conti,i)= 0.65d0
+c a_chuj(2,2,num_conti,i)= 0.50d0
+c else if (i.eq.2) then
+c a_chuj(1,1,num_conti,i)= 0.0d0
+c a_chuj(1,2,num_conti,i)= 0.0d0
+c a_chuj(2,1,num_conti,i)= 0.0d0
+c a_chuj(2,2,num_conti,i)= 0.0d0
+c endif
+C --- and its gradients
+cd write (iout,*) 'i',i,' j',j
+cd do kkk=1,3
+cd write (iout,*) 'iii 1 kkk',kkk
+cd write (iout,*) agg(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 2 kkk',kkk
+cd write (iout,*) aggi(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 3 kkk',kkk
+cd write (iout,*) aggi1(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 4 kkk',kkk
+cd write (iout,*) aggj(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 5 kkk',kkk
+cd write (iout,*) aggj1(kkk,:)
+cd enddo
+ kkll=0
+ do k=1,2
+ do l=1,2
+ kkll=kkll+1
+ do m=1,3
+ a_chuj_der(k,l,m,1,num_conti,i)=agg(m,kkll)
+ a_chuj_der(k,l,m,2,num_conti,i)=aggi(m,kkll)
+ a_chuj_der(k,l,m,3,num_conti,i)=aggi1(m,kkll)
+ a_chuj_der(k,l,m,4,num_conti,i)=aggj(m,kkll)
+ a_chuj_der(k,l,m,5,num_conti,i)=aggj1(m,kkll)
+c do mm=1,5
+c a_chuj_der(k,l,m,mm,num_conti,i)=0.0d0
+c enddo
+ enddo
+ enddo
+ enddo
+ ENDIF
+ IF (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) THEN
+C Calculate contact energies
+ cosa4=4.0D0*cosa
+ wij=cosa-3.0D0*cosb*cosg
+ cosbg1=cosb+cosg
+ cosbg2=cosb-cosg
+c fac3=dsqrt(-ael6i)/r0ij**3
+ fac3=dsqrt(-ael6i)*r3ij
+ ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
+ ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
+c ees0mij=0.0D0
+ ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
+ ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
+C Diagnostics. Comment out or remove after debugging!
+c ees0p(num_conti,i)=0.5D0*fac3*ees0pij
+c ees0m(num_conti,i)=0.5D0*fac3*ees0mij
+c ees0m(num_conti,i)=0.0D0
+C End diagnostics.
+c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij,
+c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont
+ facont_hb(num_conti,i)=fcont
+ if (calc_grad) then
+C Angular derivatives of the contact function
+ ees0pij1=fac3/ees0pij
+ ees0mij1=fac3/ees0mij
+ fac3p=-3.0D0*fac3*rrmij
+ ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij)
+ ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij)
+c ees0mij1=0.0D0
+ ecosa1= ees0pij1*( 1.0D0+0.5D0*wij)
+ ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1)
+ ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1)
+ ecosa2= ees0mij1*(-1.0D0+0.5D0*wij)
+ ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2)
+ ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2)
+ ecosap=ecosa1+ecosa2
+ ecosbp=ecosb1+ecosb2
+ ecosgp=ecosg1+ecosg2
+ ecosam=ecosa1-ecosa2
+ ecosbm=ecosb1-ecosb2
+ ecosgm=ecosg1-ecosg2
+C Diagnostics
+c ecosap=ecosa1
+c ecosbp=ecosb1
+c ecosgp=ecosg1
+c ecosam=0.0D0
+c ecosbm=0.0D0
+c ecosgm=0.0D0
+C End diagnostics
+ fprimcont=fprimcont/rij
+cd facont_hb(num_conti,i)=1.0D0
+C Following line is for diagnostics.
+cd fprimcont=0.0D0
+ do k=1,3
+ dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
+ dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
+ enddo
+ do k=1,3
+ gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k)
+ gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
+ enddo
+ gggp(1)=gggp(1)+ees0pijp*xj
+ gggp(2)=gggp(2)+ees0pijp*yj
+ gggp(3)=gggp(3)+ees0pijp*zj
+ gggm(1)=gggm(1)+ees0mijp*xj
+ gggm(2)=gggm(2)+ees0mijp*yj
+ gggm(3)=gggm(3)+ees0mijp*zj
+C Derivatives due to the contact function
+ gacont_hbr(1,num_conti,i)=fprimcont*xj
+ gacont_hbr(2,num_conti,i)=fprimcont*yj
+ gacont_hbr(3,num_conti,i)=fprimcont*zj
+ do k=1,3
+ ghalfp=0.5D0*gggp(k)
+ ghalfm=0.5D0*gggm(k)
+ gacontp_hb1(k,num_conti,i)=ghalfp
+ & +(ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i))
+ & + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ gacontp_hb2(k,num_conti,i)=ghalfp
+ & +(ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j))
+ & + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ gacontp_hb3(k,num_conti,i)=gggp(k)
+ gacontm_hb1(k,num_conti,i)=ghalfm
+ & +(ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i))
+ & + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ gacontm_hb2(k,num_conti,i)=ghalfm
+ & +(ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j))
+ & + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ gacontm_hb3(k,num_conti,i)=gggm(k)
+ enddo
+ endif
+C Diagnostics. Comment out or remove after debugging!
+cdiag do k=1,3
+cdiag gacontp_hb1(k,num_conti,i)=0.0D0
+cdiag gacontp_hb2(k,num_conti,i)=0.0D0
+cdiag gacontp_hb3(k,num_conti,i)=0.0D0
+cdiag gacontm_hb1(k,num_conti,i)=0.0D0
+cdiag gacontm_hb2(k,num_conti,i)=0.0D0
+cdiag gacontm_hb3(k,num_conti,i)=0.0D0
+cdiag enddo
+ ENDIF ! wcorr
+ endif ! num_conti.le.maxconts
+ endif ! fcont.gt.0
+ endif ! j.gt.i+1
+ 1216 continue
+ enddo ! j
+ num_cont_hb(i)=num_conti
+ 1215 continue
+ enddo ! i
+cd do i=1,nres
+cd write (iout,'(i3,3f10.5,5x,3f10.5)')
+cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i)
+cd enddo
+c 12/7/99 Adam eello_turn3 will be considered as a separate energy term
+ccc eel_loc=eel_loc+eello_turn3
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine eturn34(i,j,eello_turn3,eello_turn4)
+C Third- and fourth-order contributions from turns
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ dimension ggg(3)
+ double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
+ & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
+ double precision agg(3,4),aggi(3,4),aggi1(3,4),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
+ if (j.eq.i+2) then
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Third-order contributions
+C
+C (i+2)o----(i+3)
+C | |
+C | |
+C (i+1)o----i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd call checkint_turn3(i,a_temp,eello_turn3_num)
+ call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
+ call transpose2(auxmat(1,1),auxmat1(1,1))
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+cd write (2,*) 'i,',i,' j',j,'eello_turn3',
+cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
+cd & ' eello_turn3_num',4*eello_turn3_num
+ if (calc_grad) then
+C Derivatives in gamma(i)
+ call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1))
+ call transpose2(auxmat2(1,1),pizda(1,1))
+ call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
+ gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
+C Derivatives in gamma(i+1)
+ call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
+ call transpose2(auxmat2(1,1),pizda(1,1))
+ call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
+ gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+C Cartesian derivatives
+ do l=1,3
+ a_temp(1,1)=aggi(l,1)
+ a_temp(1,2)=aggi(l,2)
+ a_temp(2,1)=aggi(l,3)
+ a_temp(2,2)=aggi(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,i)=gcorr3_turn(l,i)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggi1(l,1)
+ a_temp(1,2)=aggi1(l,2)
+ a_temp(2,1)=aggi1(l,3)
+ a_temp(2,2)=aggi1(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggj(l,1)
+ a_temp(1,2)=aggj(l,2)
+ a_temp(2,1)=aggj(l,3)
+ a_temp(2,2)=aggj(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,j)=gcorr3_turn(l,j)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggj1(l,1)
+ a_temp(1,2)=aggj1(l,2)
+ a_temp(2,1)=aggj1(l,3)
+ a_temp(2,2)=aggj1(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ enddo
+ endif
+ else if (j.eq.i+3) then
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Fourth-order contributions
+C
+C (i+3)o----(i+4)
+C / |
+C (i+2)o |
+C \ |
+C (i+1)o----i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd call checkint_turn4(i,a_temp,eello_turn4_num)
+ iti1=itortyp(itype(i+1))
+ iti2=itortyp(itype(i+2))
+ iti3=itortyp(itype(i+3))
+ call transpose2(EUg(1,1,i+1),e1t(1,1))
+ call transpose2(Eug(1,1,i+2),e2t(1,1))
+ call transpose2(Eug(1,1,i+3),e3t(1,1))
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ eello_turn4=eello_turn4-(s1+s2+s3)
+cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
+cd & ' eello_turn4_num',8*eello_turn4_num
+C Derivatives in gamma(i)
+ if (calc_grad) then
+ call transpose2(EUgder(1,1,i+1),e1tder(1,1))
+ call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
+C Derivatives in gamma(i+1)
+ call transpose2(EUgder(1,1,i+2),e2tder(1,1))
+ call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1))
+ call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
+C Derivatives in gamma(i+2)
+ call transpose2(EUgder(1,1,i+3),e3tder(1,1))
+ call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1))
+ call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
+C Cartesian derivatives
+C Derivatives of this turn contributions in DC(i+2)
+ if (j.lt.nres-1) then
+ do l=1,3
+ a_temp(1,1)=agg(l,1)
+ a_temp(1,2)=agg(l,2)
+ a_temp(2,1)=agg(l,3)
+ a_temp(2,2)=agg(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ ggg(l)=-(s1+s2+s3)
+ gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
+ enddo
+ endif
+C Remaining derivatives of this turn contribution
+ do l=1,3
+ a_temp(1,1)=aggi(l,1)
+ a_temp(1,2)=aggi(l,2)
+ a_temp(2,1)=aggi(l,3)
+ a_temp(2,2)=aggi(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
+ a_temp(1,1)=aggi1(l,1)
+ a_temp(1,2)=aggi1(l,2)
+ a_temp(2,1)=aggi1(l,3)
+ a_temp(2,2)=aggi1(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
+ a_temp(1,1)=aggj(l,1)
+ a_temp(1,2)=aggj(l,2)
+ a_temp(2,1)=aggj(l,3)
+ a_temp(2,2)=aggj(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
+ a_temp(1,1)=aggj1(l,1)
+ a_temp(1,2)=aggj1(l,2)
+ a_temp(2,1)=aggj1(l,3)
+ a_temp(2,2)=aggj1(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
+ enddo
+ endif
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine vecpr(u,v,w)
+ implicit real*8(a-h,o-z)
+ dimension u(3),v(3),w(3)
+ w(1)=u(2)*v(3)-u(3)*v(2)
+ w(2)=-u(1)*v(3)+u(3)*v(1)
+ w(3)=u(1)*v(2)-u(2)*v(1)
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine unormderiv(u,ugrad,unorm,ungrad)
+C This subroutine computes the derivatives of a normalized vector u, given
+C the derivatives computed without normalization conditions, ugrad. Returns
+C ungrad.
+ implicit none
+ double precision u(3),ugrad(3,3),unorm,ungrad(3,3)
+ double precision vec(3)
+ double precision scalar
+ integer i,j
+c write (2,*) 'ugrad',ugrad
+c write (2,*) 'u',u
+ do i=1,3
+ vec(i)=scalar(ugrad(1,i),u(1))
+ enddo
+c write (2,*) 'vec',vec
+ do i=1,3
+ do j=1,3
+ ungrad(j,i)=(ugrad(j,i)-u(j)*vec(i))*unorm
+ enddo
+ enddo
+c write (2,*) 'ungrad',ungrad
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine escp(evdw2,evdw2_14)
+C
+C This subroutine calculates the excluded-volume interaction energy between
+C peptide-group centers and side chains and its gradient in virtual-bond and
+C side-chain vectors.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.FFIELD'
+ include 'COMMON.IOUNITS'
+ dimension ggg(3)
+ evdw2=0.0D0
+ evdw2_14=0.0d0
+cd print '(a)','Enter ESCP'
+c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
+c & ' scal14',scal14
+ do i=iatscp_s,iatscp_e
+ iteli=itel(i)
+c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
+c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
+ if (iteli.eq.0) goto 1225
+ xi=0.5D0*(c(1,i)+c(1,i+1))
+ yi=0.5D0*(c(2,i)+c(2,i+1))
+ zi=0.5D0*(c(3,i)+c(3,i+1))
+
+ do iint=1,nscp_gr(i)
+
+ do j=iscpstart(i,iint),iscpend(i,iint)
+ itypj=itype(j)
+C Uncomment following three lines for SC-p interactions
+c xj=c(1,nres+j)-xi
+c yj=c(2,nres+j)-yi
+c zj=c(3,nres+j)-zi
+C Uncomment following three lines for Ca-p interactions
+ xj=c(1,j)-xi
+ yj=c(2,j)-yi
+ zj=c(3,j)-zi
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ fac=rrij**expon2
+ e1=fac*fac*aad(itypj,iteli)
+ e2=fac*bad(itypj,iteli)
+ if (iabs(j-i) .le. 2) then
+ e1=scal14*e1
+ e2=scal14*e2
+ evdw2_14=evdw2_14+e1+e2
+ endif
+ evdwij=e1+e2
+c write (iout,*) i,j,evdwij
+ evdw2=evdw2+evdwij
+ if (calc_grad) then
+C
+C Calculate contributions to the gradient in the virtual-bond and SC vectors.
+C
+ fac=-(evdwij+e1)*rrij
+ ggg(1)=xj*fac
+ ggg(2)=yj*fac
+ ggg(3)=zj*fac
+ if (j.lt.i) then
+cd write (iout,*) 'j<i'
+C Uncomment following three lines for SC-p interactions
+c do k=1,3
+c gradx_scp(k,j)=gradx_scp(k,j)+ggg(k)
+c enddo
+ else
+cd write (iout,*) 'j>i'
+ do k=1,3
+ ggg(k)=-ggg(k)
+C Uncomment following line for SC-p interactions
+c gradx_scp(k,j)=gradx_scp(k,j)-ggg(k)
+ enddo
+ endif
+ do k=1,3
+ gvdwc_scp(k,i)=gvdwc_scp(k,i)-0.5D0*ggg(k)
+ enddo
+ kstart=min0(i+1,j)
+ kend=max0(i-1,j-1)
+cd write (iout,*) 'i=',i,' j=',j,' kstart=',kstart,' kend=',kend
+cd write (iout,*) ggg(1),ggg(2),ggg(3)
+ do k=kstart,kend
+ do l=1,3
+ gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l)
+ enddo
+ enddo
+ endif
+ enddo
+ enddo ! iint
+ 1225 continue
+ enddo ! i
+ do i=1,nct
+ do j=1,3
+ gvdwc_scp(j,i)=expon*gvdwc_scp(j,i)
+ gradx_scp(j,i)=expon*gradx_scp(j,i)
+ enddo
+ enddo
+C******************************************************************************
+C
+C N O T E !!!
+C
+C To save time the factor EXPON has been extracted from ALL components
+C of GVDWC and GRADX. Remember to multiply them by this factor before further
+C use!
+C
+C******************************************************************************
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine edis(ehpb)
+C
+C Evaluate bridge-strain energy and its gradient in virtual-bond and SC vectors.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ dimension ggg(3)
+ ehpb=0.0D0
+cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
+cd write(iout,*)'link_start=',link_start,' link_end=',link_end
+ if (link_end.eq.0) return
+ do i=link_start,link_end
+C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
+C CA-CA distance used in regularization of structure.
+ ii=ihpb(i)
+ jj=jhpb(i)
+C iii and jjj point to the residues for which the distance is assigned.
+ if (ii.gt.nres) then
+ iii=ii-nres
+ jjj=jj-nres
+ else
+ iii=ii
+ jjj=jj
+ endif
+c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c & dhpb(i),dhpb1(i),forcon(i)
+C 24/11/03 AL: SS bridges handled separately because of introducing a specific
+C distance and angle dependent SS bond potential.
+ if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+ call ssbond_ene(iii,jjj,eij)
+ ehpb=ehpb+2*eij
+cd write (iout,*) "eij",eij
+ else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "beta nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
+ else
+C Calculate the distance between the two points and its difference from the
+C target distance.
+ dd=dist(ii,jj)
+ if (dhpb1(i).gt.0.0d0) then
+ ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c write (iout,*) "alph nmr",
+c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+ else
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+c write (iout,*) "alpha reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+ endif
+cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
+cd & ' waga=',waga,' fac=',fac
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
+C If this is a SC-SC distance, we need to calculate the contributions to the
+C Cartesian gradient in the SC vectors (ghpbx).
+ if (iii.lt.ii) then
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ endif
+ do k=1,3
+ ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+ ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+ enddo
+ endif
+ enddo
+ ehpb=0.5D0*ehpb
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine ssbond_ene(i,j,eij)
+C
+C Calculate the distance and angle dependent SS-bond potential energy
+C using a free-energy function derived based on RHF/6-31G** ab initio
+C calculations of diethyl disulfide.
+C
+C A. Liwo and U. Kozlowska, 11/24/03
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+ double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
+ itypi=itype(i)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=dsc_inv(itypi)
+ itypj=itype(j)
+ dscj_inv=dsc_inv(itypj)
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+ erij(1)=xj*rij
+ erij(2)=yj*rij
+ erij(3)=zj*rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ do k=1,3
+ dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
+ dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
+ enddo
+ rij=1.0d0/rij
+ deltad=rij-d0cm
+ deltat1=1.0d0-om1
+ deltat2=1.0d0+om2
+ deltat12=om2-om1+2.0d0
+ cosphi=om12-om1*om2
+ eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
+ & +akct*deltad*deltat12
+ & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
+c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
+c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
+c & " deltat12",deltat12," eij",eij
+ ed=2*akcm*deltad+akct*deltat12
+ pom1=akct*deltad
+ pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
+ eom1=-2*akth*deltat1-pom1-om2*pom2
+ eom2= 2*akth*deltat2+pom1-om1*pom2
+ eom12=pom2
+ do k=1,3
+ gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+ enddo
+ do k=1,3
+ ghpbx(k,i)=ghpbx(k,i)-gg(k)
+ & +(eom12*dc_norm(k,nres+j)+eom1*erij(k))*dsci_inv
+ ghpbx(k,j)=ghpbx(k,j)+gg(k)
+ & +(eom12*dc_norm(k,nres+i)+eom2*erij(k))*dscj_inv
+ enddo
+C
+C Calculate the components of the gradient in DC and X
+C
+ do k=i,j-1
+ do l=1,3
+ ghpbc(l,k)=ghpbc(l,k)+gg(l)
+ enddo
+ enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine ebond(estr)
+c
+c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds
+c
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ include 'COMMON.CONTROL'
+ double precision u(3),ud(3)
+ estr=0.0d0
+ do i=nnt+1,nct
+ diff = vbld(i)-vbldp0
+c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
+ estr=estr+diff*diff
+ do j=1,3
+ gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i)
+ enddo
+ enddo
+ estr=0.5d0*AKP*estr
+c
+c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
+c
+ do i=nnt,nct
+ iti=itype(i)
+ if (iti.ne.10) then
+ nbi=nbondterm(iti)
+ if (nbi.eq.1) then
+ diff=vbld(i+nres)-vbldsc0(1,iti)
+c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
+c & AKSC(1,iti),AKSC(1,iti)*diff*diff
+ estr=estr+0.5d0*AKSC(1,iti)*diff*diff
+ do j=1,3
+ gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
+ enddo
+ else
+ do j=1,nbi
+ diff=vbld(i+nres)-vbldsc0(j,iti)
+ ud(j)=aksc(j,iti)*diff
+ u(j)=abond0(j,iti)+0.5d0*ud(j)*diff
+ enddo
+ uprod=u(1)
+ do j=2,nbi
+ uprod=uprod*u(j)
+ enddo
+ usum=0.0d0
+ usumsqder=0.0d0
+ do j=1,nbi
+ uprod1=1.0d0
+ uprod2=1.0d0
+ do k=1,nbi
+ if (k.ne.j) then
+ uprod1=uprod1*u(k)
+ uprod2=uprod2*u(k)*u(k)
+ endif
+ enddo
+ usum=usum+uprod1
+ usumsqder=usumsqder+ud(j)*uprod2
+ enddo
+c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti),
+c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi)
+ estr=estr+uprod/usum
+ do j=1,3
+ gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
+ enddo
+ endif
+ endif
+ enddo
+ return
+ end
+#ifdef CRYST_THETA
+C--------------------------------------------------------------------------
+ subroutine ebend(etheta)
+C
+C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
+C angles gamma and its derivatives in consecutive thetas and gammas.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+ double precision y(2),z(2)
+ delta=0.02d0*pi
+ time11=dexp(-2*time)
+ time12=1.0d0
+ etheta=0.0D0
+c write (iout,*) "nres",nres
+c write (*,'(a,i2)') 'EBEND ICG=',icg
+c write (iout,*) ithet_start,ithet_end
+ do i=ithet_start,ithet_end
+C Zero the energy function and its derivative at 0 or pi.
+ call splinthet(theta(i),0.5d0*delta,ss,ssd)
+ it=itype(i-1)
+c if (i.gt.ithet_start .and.
+c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
+c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
+c phii=phi(i)
+c y(1)=dcos(phii)
+c y(2)=dsin(phii)
+c else
+c y(1)=0.0D0
+c y(2)=0.0D0
+c endif
+c if (i.lt.nres .and. itel(i).ne.0) then
+c phii1=phi(i+1)
+c z(1)=dcos(phii1)
+c z(2)=dsin(phii1)
+c else
+c z(1)=0.0D0
+c z(2)=0.0D0
+c endif
+ if (i.gt.3) then
+#ifdef OSF
+ phii=phi(i)
+ icrc=0
+ call proc_proc(phii,icrc)
+ if (icrc.eq.1) phii=150.0
+#else
+ phii=phi(i)
+#endif
+ y(1)=dcos(phii)
+ y(2)=dsin(phii)
+ else
+ y(1)=0.0D0
+ y(2)=0.0D0
+ endif
+ if (i.lt.nres) then
+#ifdef OSF
+ phii1=phi(i+1)
+ icrc=0
+ call proc_proc(phii1,icrc)
+ if (icrc.eq.1) phii1=150.0
+ phii1=pinorm(phii1)
+ z(1)=cos(phii1)
+#else
+ phii1=phi(i+1)
+ z(1)=dcos(phii1)
+#endif
+ z(2)=dsin(phii1)
+ else
+ z(1)=0.0D0
+ z(2)=0.0D0
+ endif
+C Calculate the "mean" value of theta from the part of the distribution
+C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2).
+C In following comments this theta will be referred to as t_c.
+ thet_pred_mean=0.0d0
+ do k=1,2
+ athetk=athet(k,it)
+ bthetk=bthet(k,it)
+ thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+ enddo
+c write (iout,*) "thet_pred_mean",thet_pred_mean
+ dthett=thet_pred_mean*ssd
+ thet_pred_mean=thet_pred_mean*ss+a0thet(it)
+c write (iout,*) "thet_pred_mean",thet_pred_mean
+C Derivatives of the "mean" values in gamma1 and gamma2.
+ dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
+ dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ if (theta(i).gt.pi-delta) then
+ call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
+ & E_tc0)
+ call mixder(pi-delta,thet_pred_mean,theta0(it),fprim_tc0)
+ call theteng(pi,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
+ call spline1(theta(i),pi-delta,delta,f0,f1,fprim0,ethetai,
+ & E_theta)
+ call spline2(theta(i),pi-delta,delta,E_tc0,E_tc1,fprim_tc0,
+ & E_tc)
+ else if (theta(i).lt.delta) then
+ call theteng(delta,thet_pred_mean,theta0(it),f0,fprim0,E_tc0)
+ call theteng(0.0d0,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
+ call spline1(theta(i),delta,-delta,f0,f1,fprim0,ethetai,
+ & E_theta)
+ call mixder(delta,thet_pred_mean,theta0(it),fprim_tc0)
+ call spline2(theta(i),delta,-delta,E_tc0,E_tc1,fprim_tc0,
+ & E_tc)
+ else
+ call theteng(theta(i),thet_pred_mean,theta0(it),ethetai,
+ & E_theta,E_tc)
+ endif
+ etheta=etheta+ethetai
+c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i),
+c & rad2deg*phii,rad2deg*phii1,ethetai
+ if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
+ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
+ gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
+ 1215 continue
+ enddo
+C Ufff.... We've done all this!!!
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine theteng(thetai,thet_pred_mean,theta0i,ethetai,E_theta,
+ & E_tc)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+C Calculate the contributions to both Gaussian lobes.
+C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time)
+C The "polynomial part" of the "standard deviation" of this part of
+C the distribution.
+ sig=polthet(3,it)
+ do j=2,0,-1
+ sig=sig*thet_pred_mean+polthet(j,it)
+ enddo
+C Derivative of the "interior part" of the "standard deviation of the"
+C gamma-dependent Gaussian lobe in t_c.
+ sigtc=3*polthet(3,it)
+ do j=2,1,-1
+ sigtc=sigtc*thet_pred_mean+j*polthet(j,it)
+ enddo
+ sigtc=sig*sigtc
+C Set the parameters of both Gaussian lobes of the distribution.
+C "Standard deviation" of the gamma-dependent Gaussian lobe (sigtc)
+ fac=sig*sig+sigc0(it)
+ sigcsq=fac+fac
+ sigc=1.0D0/sigcsq
+C Following variable (sigsqtc) is -(1/2)d[sigma(t_c)**(-2))]/dt_c
+ sigsqtc=-4.0D0*sigcsq*sigtc
+c print *,i,sig,sigtc,sigsqtc
+C Following variable (sigtc) is d[sigma(t_c)]/dt_c
+ sigtc=-sigtc/(fac*fac)
+C Following variable is sigma(t_c)**(-2)
+ sigcsq=sigcsq*sigcsq
+ sig0i=sig0(it)
+ sig0inv=1.0D0/sig0i**2
+ delthec=thetai-thet_pred_mean
+ delthe0=thetai-theta0i
+ term1=-0.5D0*sigcsq*delthec*delthec
+ term2=-0.5D0*sig0inv*delthe0*delthe0
+C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and
+C NaNs in taking the logarithm. We extract the largest exponent which is added
+C to the energy (this being the log of the distribution) at the end of energy
+C term evaluation for this virtual-bond angle.
+ if (term1.gt.term2) then
+ termm=term1
+ term2=dexp(term2-termm)
+ term1=1.0d0
+ else
+ termm=term2
+ term1=dexp(term1-termm)
+ term2=1.0d0
+ endif
+C The ratio between the gamma-independent and gamma-dependent lobes of
+C the distribution is a Gaussian function of thet_pred_mean too.
+ diffak=gthet(2,it)-thet_pred_mean
+ ratak=diffak/gthet(3,it)**2
+ ak=dexp(gthet(1,it)-0.5D0*diffak*ratak)
+C Let's differentiate it in thet_pred_mean NOW.
+ aktc=ak*ratak
+C Now put together the distribution terms to make complete distribution.
+ termexp=term1+ak*term2
+ termpre=sigc+ak*sig0i
+C Contribution of the bending energy from this theta is just the -log of
+C the sum of the contributions from the two lobes and the pre-exponential
+C factor. Simple enough, isn't it?
+ ethetai=(-dlog(termexp)-termm+dlog(termpre))
+C NOW the derivatives!!!
+C 6/6/97 Take into account the deformation.
+ E_theta=(delthec*sigcsq*term1
+ & +ak*delthe0*sig0inv*term2)/termexp
+ E_tc=((sigtc+aktc*sig0i)/termpre
+ & -((delthec*sigcsq+delthec*delthec*sigsqtc)*term1+
+ & aktc*term2)/termexp)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine mixder(thetai,thet_pred_mean,theta0i,E_tc_t)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+ delthec=thetai-thet_pred_mean
+ delthe0=thetai-theta0i
+C "Thank you" to MAPLE (probably spared one day of hand-differentiation).
+ t3 = thetai-thet_pred_mean
+ t6 = t3**2
+ t9 = term1
+ t12 = t3*sigcsq
+ t14 = t12+t6*sigsqtc
+ t16 = 1.0d0
+ t21 = thetai-theta0i
+ t23 = t21**2
+ t26 = term2
+ t27 = t21*t26
+ t32 = termexp
+ t40 = t32**2
+ E_tc_t = -((sigcsq+2.D0*t3*sigsqtc)*t9-t14*sigcsq*t3*t16*t9
+ & -aktc*sig0inv*t27)/t32+(t14*t9+aktc*t26)/t40
+ & *(-t12*t9-ak*sig0inv*t27)
+ return
+ end
+#else
+C--------------------------------------------------------------------------
+ subroutine ebend(etheta)
+C
+C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
+C angles gamma and its derivatives in consecutive thetas and gammas.
+C ab initio-derived potentials from
+c Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ include 'COMMON.CONTROL'
+ double precision coskt(mmaxtheterm),sinkt(mmaxtheterm),
+ & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle),
+ & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble),
+ & sinph1ph2(maxdouble,maxdouble)
+ logical lprn /.false./, lprn1 /.false./
+ etheta=0.0D0
+c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
+ do i=ithet_start,ithet_end
+ dethetai=0.0d0
+ dephii=0.0d0
+ dephii1=0.0d0
+ theti2=0.5d0*theta(i)
+ ityp2=ithetyp(itype(i-1))
+ do k=1,nntheterm
+ coskt(k)=dcos(k*theti2)
+ sinkt(k)=dsin(k*theti2)
+ enddo
+ if (i.gt.3) then
+#ifdef OSF
+ phii=phi(i)
+ if (phii.ne.phii) phii=150.0
+#else
+ phii=phi(i)
+#endif
+ ityp1=ithetyp(itype(i-2))
+ do k=1,nsingle
+ cosph1(k)=dcos(k*phii)
+ sinph1(k)=dsin(k*phii)
+ enddo
+ else
+ phii=0.0d0
+ ityp1=nthetyp+1
+ do k=1,nsingle
+ cosph1(k)=0.0d0
+ sinph1(k)=0.0d0
+ enddo
+ endif
+ if (i.lt.nres) then
+#ifdef OSF
+ phii1=phi(i+1)
+ if (phii1.ne.phii1) phii1=150.0
+ phii1=pinorm(phii1)
+#else
+ phii1=phi(i+1)
+#endif
+ ityp3=ithetyp(itype(i))
+ do k=1,nsingle
+ cosph2(k)=dcos(k*phii1)
+ sinph2(k)=dsin(k*phii1)
+ enddo
+ else
+ phii1=0.0d0
+ ityp3=nthetyp+1
+ do k=1,nsingle
+ cosph2(k)=0.0d0
+ sinph2(k)=0.0d0
+ enddo
+ endif
+c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
+c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
+c call flush(iout)
+ ethetai=aa0thet(ityp1,ityp2,ityp3)
+ do k=1,ndouble
+ do l=1,k-1
+ ccl=cosph1(l)*cosph2(k-l)
+ ssl=sinph1(l)*sinph2(k-l)
+ scl=sinph1(l)*cosph2(k-l)
+ csl=cosph1(l)*sinph2(k-l)
+ cosph1ph2(l,k)=ccl-ssl
+ cosph1ph2(k,l)=ccl+ssl
+ sinph1ph2(l,k)=scl+csl
+ sinph1ph2(k,l)=scl-csl
+ enddo
+ enddo
+ if (lprn) then
+ write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,
+ & " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
+ write (iout,*) "coskt and sinkt"
+ do k=1,nntheterm
+ write (iout,*) k,coskt(k),sinkt(k)
+ enddo
+ endif
+ do k=1,ntheterm
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ & *coskt(k)
+ if (lprn)
+ & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & " ethetai",ethetai
+ enddo
+ if (lprn) then
+ write (iout,*) "cosph and sinph"
+ do k=1,nsingle
+ write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
+ enddo
+ write (iout,*) "cosph1ph2 and sinph2ph2"
+ do k=2,ndouble
+ do l=1,k-1
+ write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),
+ & sinph1ph2(l,k),sinph1ph2(k,l)
+ enddo
+ enddo
+ write(iout,*) "ethetai",ethetai
+ endif
+ do m=1,ntheterm2
+ do k=1,nsingle
+ aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ ethetai=ethetai+sinkt(m)*aux
+ dethetai=dethetai+0.5d0*m*aux*coskt(m)
+ dephii=dephii+k*sinkt(m)*(
+ & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ dephii1=dephii1+k*sinkt(m)*(
+ & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ if (lprn)
+ & write (iout,*) "m",m," k",k," bbthet",
+ & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
+ & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
+ & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
+ & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ enddo
+ enddo
+ if (lprn)
+ & write(iout,*) "ethetai",ethetai
+ do m=1,ntheterm3
+ do k=2,ndouble
+ do l=1,k-1
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ ethetai=ethetai+sinkt(m)*aux
+ dethetai=dethetai+0.5d0*m*coskt(m)*aux
+ dephii=dephii+l*sinkt(m)*(
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ dephii1=dephii1+(k-l)*sinkt(m)*(
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ if (lprn) then
+ write (iout,*) "m",m," k",k," l",l," ffthet",
+ & ffthet(l,k,m,ityp1,ityp2,ityp3),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ write (iout,*) cosph1ph2(l,k)*sinkt(m),
+ & cosph1ph2(k,l)*sinkt(m),
+ & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
+ endif
+ enddo
+ enddo
+ enddo
+10 continue
+ if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)')
+ & i,theta(i)*rad2deg,phii*rad2deg,
+ & phii1*rad2deg,ethetai
+ etheta=etheta+ethetai
+ if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
+ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
+ gloc(nphi+i-2,icg)=wang*dethetai
+ enddo
+ return
+ end
+#endif
+#ifdef CRYST_SC
+c-----------------------------------------------------------------------------
+ subroutine esc(escloc)
+C Calculate the local energy of a side chain and its derivatives in the
+C corresponding virtual-bond valence angles THETA and the spherical angles
+C ALPHA and OMEGA.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ double precision x(3),dersc(3),xemp(3),dersc0(3),dersc1(3),
+ & ddersc0(3),ddummy(3),xtemp(3),temp(3)
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ delta=0.02d0*pi
+ escloc=0.0D0
+c write (iout,'(a)') 'ESC'
+ do i=loc_start,loc_end
+ it=itype(i)
+ if (it.eq.10) goto 1
+ nlobit=nlob(it)
+c print *,'i=',i,' it=',it,' nlobit=',nlobit
+c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
+ theti=theta(i+1)-pipol
+ x(1)=dtan(theti)
+ x(2)=alph(i)
+ x(3)=omeg(i)
+c write (iout,*) "i",i," x",x(1),x(2),x(3)
+
+ if (x(2).gt.pi-delta) then
+ xtemp(1)=x(1)
+ xtemp(2)=pi-delta
+ xtemp(3)=x(3)
+ call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
+ xtemp(2)=pi
+ call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
+ call spline1(x(2),pi-delta,delta,escloci0,escloci1,dersc0(2),
+ & escloci,dersc(2))
+ call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
+ & ddersc0(1),dersc(1))
+ call spline2(x(2),pi-delta,delta,dersc0(3),dersc1(3),
+ & ddersc0(3),dersc(3))
+ xtemp(2)=pi-delta
+ call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
+ xtemp(2)=pi
+ call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
+ call spline1(x(2),pi-delta,delta,esclocbi0,esclocbi1,
+ & dersc0(2),esclocbi,dersc02)
+ call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
+ & dersc12,dersc01)
+ call splinthet(x(2),0.5d0*delta,ss,ssd)
+ dersc0(1)=dersc01
+ dersc0(2)=dersc02
+ dersc0(3)=0.0d0
+ do k=1,3
+ dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
+ enddo
+ dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
+c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
+c & esclocbi,ss,ssd
+ escloci=ss*escloci+(1.0d0-ss)*esclocbi
+c escloci=esclocbi
+c write (iout,*) escloci
+ else if (x(2).lt.delta) then
+ xtemp(1)=x(1)
+ xtemp(2)=delta
+ xtemp(3)=x(3)
+ call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
+ xtemp(2)=0.0d0
+ call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
+ call spline1(x(2),delta,-delta,escloci0,escloci1,dersc0(2),
+ & escloci,dersc(2))
+ call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
+ & ddersc0(1),dersc(1))
+ call spline2(x(2),delta,-delta,dersc0(3),dersc1(3),
+ & ddersc0(3),dersc(3))
+ xtemp(2)=delta
+ call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
+ xtemp(2)=0.0d0
+ call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
+ call spline1(x(2),delta,-delta,esclocbi0,esclocbi1,
+ & dersc0(2),esclocbi,dersc02)
+ call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
+ & dersc12,dersc01)
+ dersc0(1)=dersc01
+ dersc0(2)=dersc02
+ dersc0(3)=0.0d0
+ call splinthet(x(2),0.5d0*delta,ss,ssd)
+ do k=1,3
+ dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
+ enddo
+ dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
+c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
+c & esclocbi,ss,ssd
+ escloci=ss*escloci+(1.0d0-ss)*esclocbi
+c write (iout,*) escloci
+ else
+ call enesc(x,escloci,dersc,ddummy,.false.)
+ endif
+
+ escloc=escloc+escloci
+c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
+
+ gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
+ & wscloc*dersc(1)
+ gloc(ialph(i,1),icg)=wscloc*dersc(2)
+ gloc(ialph(i,1)+nside,icg)=wscloc*dersc(3)
+ 1 continue
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine enesc(x,escloci,dersc,ddersc,mixed)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ double precision x(3),z(3),Ax(3,maxlob,-1:1),dersc(3),ddersc(3)
+ double precision contr(maxlob,-1:1)
+ logical mixed
+c write (iout,*) 'it=',it,' nlobit=',nlobit
+ escloc_i=0.0D0
+ do j=1,3
+ dersc(j)=0.0D0
+ if (mixed) ddersc(j)=0.0d0
+ enddo
+ x3=x(3)
+
+C Because of periodicity of the dependence of the SC energy in omega we have
+C to add up the contributions from x(3)-2*pi, x(3), and x(3+2*pi).
+C To avoid underflows, first compute & store the exponents.
+
+ do iii=-1,1
+
+ x(3)=x3+iii*dwapi
+
+ do j=1,nlobit
+ do k=1,3
+ z(k)=x(k)-censc(k,j,it)
+ enddo
+ do k=1,3
+ Axk=0.0D0
+ do l=1,3
+ Axk=Axk+gaussc(l,k,j,it)*z(l)
+ enddo
+ Ax(k,j,iii)=Axk
+ enddo
+ expfac=0.0D0
+ do k=1,3
+ expfac=expfac+Ax(k,j,iii)*z(k)
+ enddo
+ contr(j,iii)=expfac
+ enddo ! j
+
+ enddo ! iii
+
+ x(3)=x3
+C As in the case of ebend, we want to avoid underflows in exponentiation and
+C subsequent NaNs and INFs in energy calculation.
+C Find the largest exponent
+ emin=contr(1,-1)
+ do iii=-1,1
+ do j=1,nlobit
+ if (emin.gt.contr(j,iii)) emin=contr(j,iii)
+ enddo
+ enddo
+ emin=0.5D0*emin
+cd print *,'it=',it,' emin=',emin
+
+C Compute the contribution to SC energy and derivatives
+ do iii=-1,1
+
+ do j=1,nlobit
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+cd print *,'j=',j,' expfac=',expfac
+ escloc_i=escloc_i+expfac
+ do k=1,3
+ dersc(k)=dersc(k)+Ax(k,j,iii)*expfac
+ enddo
+ if (mixed) then
+ do k=1,3,2
+ ddersc(k)=ddersc(k)+(-Ax(2,j,iii)*Ax(k,j,iii)
+ & +gaussc(k,2,j,it))*expfac
+ enddo
+ endif
+ enddo
+
+ enddo ! iii
+
+ dersc(1)=dersc(1)/cos(theti)**2
+ ddersc(1)=ddersc(1)/cos(theti)**2
+ ddersc(3)=ddersc(3)
+
+ escloci=-(dlog(escloc_i)-emin)
+ do j=1,3
+ dersc(j)=dersc(j)/escloc_i
+ enddo
+ if (mixed) then
+ do j=1,3,2
+ ddersc(j)=(ddersc(j)/escloc_i+dersc(2)*dersc(j))
+ enddo
+ endif
+ return
+ end
+C------------------------------------------------------------------------------
+ subroutine enesc_bound(x,escloci,dersc,dersc12,mixed)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ double precision x(3),z(3),Ax(3,maxlob),dersc(3)
+ double precision contr(maxlob)
+ logical mixed
+
+ escloc_i=0.0D0
+
+ do j=1,3
+ dersc(j)=0.0D0
+ enddo
+
+ do j=1,nlobit
+ do k=1,2
+ z(k)=x(k)-censc(k,j,it)
+ enddo
+ z(3)=dwapi
+ do k=1,3
+ Axk=0.0D0
+ do l=1,3
+ Axk=Axk+gaussc(l,k,j,it)*z(l)
+ enddo
+ Ax(k,j)=Axk
+ enddo
+ expfac=0.0D0
+ do k=1,3
+ expfac=expfac+Ax(k,j)*z(k)
+ enddo
+ contr(j)=expfac
+ enddo ! j
+
+C As in the case of ebend, we want to avoid underflows in exponentiation and
+C subsequent NaNs and INFs in energy calculation.
+C Find the largest exponent
+ emin=contr(1)
+ do j=1,nlobit
+ if (emin.gt.contr(j)) emin=contr(j)
+ enddo
+ emin=0.5D0*emin
+
+C Compute the contribution to SC energy and derivatives
+
+ dersc12=0.0d0
+ do j=1,nlobit
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ escloc_i=escloc_i+expfac
+ do k=1,2
+ dersc(k)=dersc(k)+Ax(k,j)*expfac
+ enddo
+ if (mixed) dersc12=dersc12+(-Ax(2,j)*Ax(1,j)
+ & +gaussc(1,2,j,it))*expfac
+ dersc(3)=0.0d0
+ enddo
+
+ dersc(1)=dersc(1)/cos(theti)**2
+ dersc12=dersc12/cos(theti)**2
+ escloci=-(dlog(escloc_i)-emin)
+ do j=1,2
+ dersc(j)=dersc(j)/escloc_i
+ enddo
+ if (mixed) dersc12=(dersc12/escloc_i+dersc(2)*dersc(1))
+ return
+ end
+#else
+c----------------------------------------------------------------------------------
+ subroutine esc(escloc)
+C Calculate the local energy of a side chain and its derivatives in the
+C corresponding virtual-bond valence angles THETA and the spherical angles
+C ALPHA and OMEGA derived from AM1 all-atom calculations.
+C added by Urszula Kozlowska. 07/11/2007
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.SCROT'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ include 'COMMON.CONTROL'
+ include 'COMMON.VECTORS'
+ double precision x_prime(3),y_prime(3),z_prime(3)
+ & , sumene,dsc_i,dp2_i,x(65),
+ & xx,yy,zz,sumene1,sumene2,sumene3,sumene4,s1,s1_6,s2,s2_6,
+ & de_dxx,de_dyy,de_dzz,de_dt
+ double precision s1_t,s1_6_t,s2_t,s2_6_t
+ double precision
+ & dXX_Ci1(3),dYY_Ci1(3),dZZ_Ci1(3),dXX_Ci(3),
+ & dYY_Ci(3),dZZ_Ci(3),dXX_XYZ(3),dYY_XYZ(3),dZZ_XYZ(3),
+ & dt_dCi(3),dt_dCi1(3)
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ delta=0.02d0*pi
+ escloc=0.0D0
+ do i=loc_start,loc_end
+ costtab(i+1) =dcos(theta(i+1))
+ sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
+ cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
+ sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
+ cosfac2=0.5d0/(1.0d0+costtab(i+1))
+ cosfac=dsqrt(cosfac2)
+ sinfac2=0.5d0/(1.0d0-costtab(i+1))
+ sinfac=dsqrt(sinfac2)
+ it=itype(i)
+ if (it.eq.10) goto 1
+c
+C Compute the axes of tghe local cartesian coordinates system; store in
+c x_prime, y_prime and z_prime
+c
+ do j=1,3
+ x_prime(j) = 0.00
+ y_prime(j) = 0.00
+ z_prime(j) = 0.00
+ enddo
+C write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres),
+C & dc_norm(3,i+nres)
+ do j = 1,3
+ x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
+ y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
+ enddo
+ do j = 1,3
+ z_prime(j) = -uz(j,i-1)
+ enddo
+c write (2,*) "i",i
+c write (2,*) "x_prime",(x_prime(j),j=1,3)
+c write (2,*) "y_prime",(y_prime(j),j=1,3)
+c write (2,*) "z_prime",(z_prime(j),j=1,3)
+c write (2,*) "xx",scalar(x_prime(1),x_prime(1)),
+c & " xy",scalar(x_prime(1),y_prime(1)),
+c & " xz",scalar(x_prime(1),z_prime(1)),
+c & " yy",scalar(y_prime(1),y_prime(1)),
+c & " yz",scalar(y_prime(1),z_prime(1)),
+c & " zz",scalar(z_prime(1),z_prime(1))
+c
+C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
+C to local coordinate system. Store in xx, yy, zz.
+c
+ xx=0.0d0
+ yy=0.0d0
+ zz=0.0d0
+ do j = 1,3
+ xx = xx + x_prime(j)*dc_norm(j,i+nres)
+ yy = yy + y_prime(j)*dc_norm(j,i+nres)
+ zz = zz + z_prime(j)*dc_norm(j,i+nres)
+ enddo
+
+ xxtab(i)=xx
+ yytab(i)=yy
+ zztab(i)=zz
+C
+C Compute the energy of the ith side cbain
+C
+c write (2,*) "xx",xx," yy",yy," zz",zz
+ it=itype(i)
+ do j = 1,65
+ x(j) = sc_parmin(j,it)
+ enddo
+#ifdef CHECK_COORD
+Cc diagnostics - remove later
+ xx1 = dcos(alph(2))
+ yy1 = dsin(alph(2))*dcos(omeg(2))
+ zz1 = -dsin(alph(2))*dsin(omeg(2))
+ write(2,'(3f8.1,3f9.3,1x,3f9.3)')
+ & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
+ & xx1,yy1,zz1
+C," --- ", xx_w,yy_w,zz_w
+c end diagnostics
+#endif
+ sumene1= x(1)+ x(2)*xx+ x(3)*yy+ x(4)*zz+ x(5)*xx**2
+ & + x(6)*yy**2+ x(7)*zz**2+ x(8)*xx*zz+ x(9)*xx*yy
+ & + x(10)*yy*zz
+ sumene2= x(11) + x(12)*xx + x(13)*yy + x(14)*zz + x(15)*xx**2
+ & + x(16)*yy**2 + x(17)*zz**2 + x(18)*xx*zz + x(19)*xx*yy
+ & + x(20)*yy*zz
+ sumene3= x(21) +x(22)*xx +x(23)*yy +x(24)*zz +x(25)*xx**2
+ & +x(26)*yy**2 +x(27)*zz**2 +x(28)*xx*zz +x(29)*xx*yy
+ & +x(30)*yy*zz +x(31)*xx**3 +x(32)*yy**3 +x(33)*zz**3
+ & +x(34)*(xx**2)*yy +x(35)*(xx**2)*zz +x(36)*(yy**2)*xx
+ & +x(37)*(yy**2)*zz +x(38)*(zz**2)*xx +x(39)*(zz**2)*yy
+ & +x(40)*xx*yy*zz
+ sumene4= x(41) +x(42)*xx +x(43)*yy +x(44)*zz +x(45)*xx**2
+ & +x(46)*yy**2 +x(47)*zz**2 +x(48)*xx*zz +x(49)*xx*yy
+ & +x(50)*yy*zz +x(51)*xx**3 +x(52)*yy**3 +x(53)*zz**3
+ & +x(54)*(xx**2)*yy +x(55)*(xx**2)*zz +x(56)*(yy**2)*xx
+ & +x(57)*(yy**2)*zz +x(58)*(zz**2)*xx +x(59)*(zz**2)*yy
+ & +x(60)*xx*yy*zz
+ dsc_i = 0.743d0+x(61)
+ dp2_i = 1.9d0+x(62)
+ dscp1=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
+ & *(xx*cost2tab(i+1)+yy*sint2tab(i+1)))
+ dscp2=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
+ & *(xx*cost2tab(i+1)-yy*sint2tab(i+1)))
+ s1=(1+x(63))/(0.1d0 + dscp1)
+ s1_6=(1+x(64))/(0.1d0 + dscp1**6)
+ s2=(1+x(65))/(0.1d0 + dscp2)
+ s2_6=(1+x(65))/(0.1d0 + dscp2**6)
+ sumene = ( sumene3*sint2tab(i+1) + sumene1)*(s1+s1_6)
+ & + (sumene4*cost2tab(i+1) +sumene2)*(s2+s2_6)
+c write(2,'(i2," sumene",7f9.3)') i,sumene1,sumene2,sumene3,
+c & sumene4,
+c & dscp1,dscp2,sumene
+c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+ escloc = escloc + sumene
+c write (2,*) "escloc",escloc
+ if (.not. calc_grad) goto 1
+#ifdef DEBUG
+C
+C This section to check the numerical derivatives of the energy of ith side
+C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
+C #define DEBUG in the code to turn it on.
+C
+ write (2,*) "sumene =",sumene
+ aincr=1.0d-7
+ xxsave=xx
+ xx=xx+aincr
+ write (2,*) xx,yy,zz
+ sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+ de_dxx_num=(sumenep-sumene)/aincr
+ xx=xxsave
+ write (2,*) "xx+ sumene from enesc=",sumenep
+ yysave=yy
+ yy=yy+aincr
+ write (2,*) xx,yy,zz
+ sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+ de_dyy_num=(sumenep-sumene)/aincr
+ yy=yysave
+ write (2,*) "yy+ sumene from enesc=",sumenep
+ zzsave=zz
+ zz=zz+aincr
+ write (2,*) xx,yy,zz
+ sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+ de_dzz_num=(sumenep-sumene)/aincr
+ zz=zzsave
+ write (2,*) "zz+ sumene from enesc=",sumenep
+ costsave=cost2tab(i+1)
+ sintsave=sint2tab(i+1)
+ cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr))
+ sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr))
+ sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
+ de_dt_num=(sumenep-sumene)/aincr
+ write (2,*) " t+ sumene from enesc=",sumenep
+ cost2tab(i+1)=costsave
+ sint2tab(i+1)=sintsave
+C End of diagnostics section.
+#endif
+C
+C Compute the gradient of esc
+C
+ pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
+ pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
+ pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
+ pom_s26=6*(1.0d0+x(65))/(0.1d0 + dscp2**6)**2
+ pom_dx=dsc_i*dp2_i*cost2tab(i+1)
+ pom_dy=dsc_i*dp2_i*sint2tab(i+1)
+ pom_dt1=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)-yy*cost2tab(i+1))
+ pom_dt2=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)+yy*cost2tab(i+1))
+ pom1=(sumene3*sint2tab(i+1)+sumene1)
+ & *(pom_s1/dscp1+pom_s16*dscp1**4)
+ pom2=(sumene4*cost2tab(i+1)+sumene2)
+ & *(pom_s2/dscp2+pom_s26*dscp2**4)
+ sumene1x=x(2)+2*x(5)*xx+x(8)*zz+ x(9)*yy
+ sumene3x=x(22)+2*x(25)*xx+x(28)*zz+x(29)*yy+3*x(31)*xx**2
+ & +2*x(34)*xx*yy +2*x(35)*xx*zz +x(36)*(yy**2) +x(38)*(zz**2)
+ & +x(40)*yy*zz
+ sumene2x=x(12)+2*x(15)*xx+x(18)*zz+ x(19)*yy
+ sumene4x=x(42)+2*x(45)*xx +x(48)*zz +x(49)*yy +3*x(51)*xx**2
+ & +2*x(54)*xx*yy+2*x(55)*xx*zz+x(56)*(yy**2)+x(58)*(zz**2)
+ & +x(60)*yy*zz
+ de_dxx =(sumene1x+sumene3x*sint2tab(i+1))*(s1+s1_6)
+ & +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
+ & +(pom1+pom2)*pom_dx
+#ifdef DEBUG
+ write(2,*), "de_dxx = ", de_dxx,de_dxx_num
+#endif
+C
+ sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
+ sumene3y=x(23) +2*x(26)*yy +x(29)*xx +x(30)*zz +3*x(32)*yy**2
+ & +x(34)*(xx**2) +2*x(36)*yy*xx +2*x(37)*yy*zz +x(39)*(zz**2)
+ & +x(40)*xx*zz
+ sumene2y=x(13) + 2*x(16)*yy + x(19)*xx + x(20)*zz
+ sumene4y=x(43)+2*x(46)*yy+x(49)*xx +x(50)*zz
+ & +3*x(52)*yy**2+x(54)*xx**2+2*x(56)*yy*xx +2*x(57)*yy*zz
+ & +x(59)*zz**2 +x(60)*xx*zz
+ de_dyy =(sumene1y+sumene3y*sint2tab(i+1))*(s1+s1_6)
+ & +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
+ & +(pom1-pom2)*pom_dy
+#ifdef DEBUG
+ write(2,*), "de_dyy = ", de_dyy,de_dyy_num
+#endif
+C
+ de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
+ & +3*x(33)*zz**2 +x(35)*xx**2 +x(37)*yy**2 +2*x(38)*zz*xx
+ & +2*x(39)*zz*yy +x(40)*xx*yy)*sint2tab(i+1)*(s1+s1_6)
+ & +(x(4) + 2*x(7)*zz+ x(8)*xx + x(10)*yy)*(s1+s1_6)
+ & +(x(44)+2*x(47)*zz +x(48)*xx +x(50)*yy +3*x(53)*zz**2
+ & +x(55)*xx**2 +x(57)*(yy**2)+2*x(58)*zz*xx +2*x(59)*zz*yy
+ & +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
+ & + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
+#ifdef DEBUG
+ write(2,*), "de_dzz = ", de_dzz,de_dzz_num
+#endif
+C
+ de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
+ & -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
+ & +pom1*pom_dt1+pom2*pom_dt2
+#ifdef DEBUG
+ write(2,*), "de_dt = ", de_dt,de_dt_num
+#endif
+c
+C
+ cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
+ cossc1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres))
+ cosfac2xx=cosfac2*xx
+ sinfac2yy=sinfac2*yy
+ do k = 1,3
+ dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*
+ & vbld_inv(i+1)
+ dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*
+ & vbld_inv(i)
+ pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1)
+ pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i)
+c write (iout,*) "i",i," k",k," pom",pom," pom1",pom1,
+c & " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k)
+c write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3),
+c & (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
+ dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx
+ dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx
+ dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy
+ dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy
+ dZZ_Ci1(k)=0.0d0
+ dZZ_Ci(k)=0.0d0
+ do j=1,3
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ enddo
+
+ dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
+ dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
+ dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
+c
+ dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
+ dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
+ enddo
+
+ do k=1,3
+ dXX_Ctab(k,i)=dXX_Ci(k)
+ dXX_C1tab(k,i)=dXX_Ci1(k)
+ dYY_Ctab(k,i)=dYY_Ci(k)
+ dYY_C1tab(k,i)=dYY_Ci1(k)
+ dZZ_Ctab(k,i)=dZZ_Ci(k)
+ dZZ_C1tab(k,i)=dZZ_Ci1(k)
+ dXX_XYZtab(k,i)=dXX_XYZ(k)
+ dYY_XYZtab(k,i)=dYY_XYZ(k)
+ dZZ_XYZtab(k,i)=dZZ_XYZ(k)
+ enddo
+
+ do k = 1,3
+c write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1",
+c & dyy_ci1(k)," dzz_ci1",dzz_ci1(k)
+c write (iout,*) "k",k," dxx_ci",dxx_ci(k)," dyy_ci",
+c & dyy_ci(k)," dzz_ci",dzz_ci(k)
+c write (iout,*) "k",k," dt_dci",dt_dci(k)," dt_dci",
+c & dt_dci(k)
+c write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ",
+c & dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k)
+ gscloc(k,i-1)=gscloc(k,i-1)+de_dxx*dxx_ci1(k)
+ & +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k)
+ gscloc(k,i)=gscloc(k,i)+de_dxx*dxx_Ci(k)
+ & +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k)
+ gsclocx(k,i)= de_dxx*dxx_XYZ(k)
+ & +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k)
+ enddo
+c write(iout,*) "ENERGY GRAD = ", (gscloc(k,i-1),k=1,3),
+c & (gscloc(k,i),k=1,3),(gsclocx(k,i),k=1,3)
+
+C to check gradient call subroutine check_grad
+
+ 1 continue
+ enddo
+ return
+ end
+#endif
+c------------------------------------------------------------------------------
+ subroutine gcont(rij,r0ij,eps0ij,delta,fcont,fprimcont)
+C
+C This procedure calculates two-body contact function g(rij) and its derivative:
+C
+C eps0ij ! x < -1
+C g(rij) = esp0ij*(-0.9375*x+0.625*x**3-0.1875*x**5) ! -1 =< x =< 1
+C 0 ! x > 1
+C
+C where x=(rij-r0ij)/delta
+C
+C rij - interbody distance, r0ij - contact distance, eps0ij - contact energy
+C
+ implicit none
+ double precision rij,r0ij,eps0ij,fcont,fprimcont
+ double precision x,x2,x4,delta
+c delta=0.02D0*r0ij
+c delta=0.2D0*r0ij
+ x=(rij-r0ij)/delta
+ if (x.lt.-1.0D0) then
+ fcont=eps0ij
+ fprimcont=0.0D0
+ else if (x.le.1.0D0) then
+ x2=x*x
+ x4=x2*x2
+ fcont=eps0ij*(x*(-0.9375D0+0.6250D0*x2-0.1875D0*x4)+0.5D0)
+ fprimcont=eps0ij * (-0.9375D0+1.8750D0*x2-0.9375D0*x4)/delta
+ else
+ fcont=0.0D0
+ fprimcont=0.0D0
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine splinthet(theti,delta,ss,ssder)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ thetup=pi-delta
+ thetlow=delta
+ if (theti.gt.pipol) then
+ call gcont(theti,thetup,1.0d0,delta,ss,ssder)
+ else
+ call gcont(-theti,-thetlow,1.0d0,delta,ss,ssder)
+ ssder=-ssder
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine spline1(x,x0,delta,f0,f1,fprim0,f,fprim)
+ implicit none
+ double precision x,x0,delta,f0,f1,fprim0,f,fprim
+ double precision ksi,ksi2,ksi3,a1,a2,a3
+ a1=fprim0*delta/(f1-f0)
+ a2=3.0d0-2.0d0*a1
+ a3=a1-2.0d0
+ ksi=(x-x0)/delta
+ ksi2=ksi*ksi
+ ksi3=ksi2*ksi
+ f=f0+(f1-f0)*ksi*(a1+ksi*(a2+a3*ksi))
+ fprim=(f1-f0)/delta*(a1+ksi*(2*a2+3*ksi*a3))
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine spline2(x,x0,delta,f0x,f1x,fprim0x,fx)
+ implicit none
+ double precision x,x0,delta,f0x,f1x,fprim0x,fx
+ double precision ksi,ksi2,ksi3,a1,a2,a3
+ ksi=(x-x0)/delta
+ ksi2=ksi*ksi
+ ksi3=ksi2*ksi
+ a1=fprim0x*delta
+ a2=3*(f1x-f0x)-2*fprim0x*delta
+ a3=fprim0x*delta-2*(f1x-f0x)
+ fx=f0x+a1*ksi+a2*ksi2+a3*ksi3
+ return
+ end
+C-----------------------------------------------------------------------------
+#ifdef CRYST_TOR
+C-----------------------------------------------------------------------------
+ subroutine etor(etors,edihcnstr,fact)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ gloci=0.0D0
+C Proline-Proline pair is a special case...
+ if (itori.eq.3 .and. itori1.eq.3) then
+ if (phii.gt.-dwapi3) then
+ cosphi=dcos(3*phii)
+ fac=1.0D0/(1.0D0-cosphi)
+ etorsi=v1(1,3,3)*fac
+ etorsi=etorsi+etorsi
+ etors=etors+etorsi-v1(1,3,3)
+ gloci=gloci-3*fac*etorsi*dsin(3*phii)
+ endif
+ do j=1,3
+ v1ij=v1(j+1,itori,itori1)
+ v2ij=v2(j+1,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+ else
+ do j=1,nterm_old
+ v1ij=v1(j,itori,itori1)
+ v2ij=v2(j,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+ endif
+ if (lprn)
+ & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
+ & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
+c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
+ enddo
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+ do i=1,ndih_constr
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=phii-phi0(i)
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ endif
+! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
+! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+ enddo
+! write (iout,*) 'edihcnstr',edihcnstr
+ return
+ end
+c------------------------------------------------------------------------------
+#else
+ subroutine etor(etors,edihcnstr,fact)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+ if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ gloci=0.0D0
+C Regular cosine and sine terms
+ do j=1,nterm(itori,itori1)
+ v1ij=v1(j,itori,itori1)
+ v2ij=v2(j,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+C Lorentz terms
+C v1
+C E = SUM ----------------------------------- - v1
+C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
+C
+ cosphi=dcos(0.5d0*phii)
+ sinphi=dsin(0.5d0*phii)
+ do j=1,nlor(itori,itori1)
+ vl1ij=vlor1(j,itori,itori1)
+ vl2ij=vlor2(j,itori,itori1)
+ vl3ij=vlor3(j,itori,itori1)
+ pom=vl2ij*cosphi+vl3ij*sinphi
+ pom1=1.0d0/(pom*pom+1.0d0)
+ etors=etors+vl1ij*pom1
+ pom=-pom*pom1*pom1
+ gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
+ enddo
+C Subtract the constant term
+ etors=etors-v0(itori,itori1)
+ if (lprn)
+ & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
+ & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
+c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
+ 1215 continue
+ enddo
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+ do i=1,ndih_constr
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=pinorm(phii-phi0(i))
+ edihi=0.0d0
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ edihi=0.25d0*ftors*difi**4
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ edihi=0.25d0*ftors*difi**4
+ else
+ difi=0.0d0
+ endif
+c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi,
+c & drange(i),edihi
+! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
+! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+ enddo
+! write (iout,*) 'edihcnstr',edihcnstr
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine etor_d(etors_d,fact2)
+C 6/23/01 Compute double torsional energy
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors_d=0.0D0
+ do i=iphi_start,iphi_end-1
+ if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
+ & goto 1215
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ itori2=itortyp(itype(i))
+ phii=phi(i)
+ phii1=phi(i+1)
+ gloci1=0.0D0
+ gloci2=0.0D0
+C Regular cosine and sine terms
+ do j=1,ntermd_1(itori,itori1,itori2)
+ v1cij=v1c(1,j,itori,itori1,itori2)
+ v1sij=v1s(1,j,itori,itori1,itori2)
+ v2cij=v1c(2,j,itori,itori1,itori2)
+ v2sij=v1s(2,j,itori,itori1,itori2)
+ cosphi1=dcos(j*phii)
+ sinphi1=dsin(j*phii)
+ cosphi2=dcos(j*phii1)
+ sinphi2=dsin(j*phii1)
+ etors_d=etors_d+v1cij*cosphi1+v1sij*sinphi1+
+ & v2cij*cosphi2+v2sij*sinphi2
+ gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
+ gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
+ enddo
+ do k=2,ntermd_2(itori,itori1,itori2)
+ do l=1,k-1
+ v1cdij = v2c(k,l,itori,itori1,itori2)
+ v2cdij = v2c(l,k,itori,itori1,itori2)
+ v1sdij = v2s(k,l,itori,itori1,itori2)
+ v2sdij = v2s(l,k,itori,itori1,itori2)
+ cosphi1p2=dcos(l*phii+(k-l)*phii1)
+ cosphi1m2=dcos(l*phii-(k-l)*phii1)
+ sinphi1p2=dsin(l*phii+(k-l)*phii1)
+ sinphi1m2=dsin(l*phii-(k-l)*phii1)
+ etors_d=etors_d+v1cdij*cosphi1p2+v2cdij*cosphi1m2+
+ & v1sdij*sinphi1p2+v2sdij*sinphi1m2
+ gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
+ & -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
+ gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
+ & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
+ enddo
+ enddo
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
+ gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*fact2*gloci2
+ 1215 continue
+ enddo
+ return
+ end
+#endif
+c------------------------------------------------------------------------------
+ subroutine eback_sc_corr(esccor)
+c 7/21/2007 Correlations between the backbone-local and side-chain-local
+c conformational states; temporarily implemented as differences
+c between UNRES torsional potentials (dependent on three types of
+c residues) and the torsional potentials dependent on all 20 types
+c of residues computed from AM1 energy surfaces of terminally-blocked
+c amino-acid residues.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.SCCOR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.CONTROL'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+c write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor
+ esccor=0.0D0
+ do i=itau_start,itau_end
+ esccor_ii=0.0D0
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
+ phii=phi(i)
+cccc Added 9 May 2012
+cc Tauangle is torsional engle depending on the value of first digit
+c(see comment below)
+cc Omicron is flat angle depending on the value of first digit
+c(see comment below)
+
+
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
+ gloci=0.0D0
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
+ & (itype(i-1).eq.21)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.21)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.21)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
+ esccor=esccor+v1ij*cosphi+v2ij*sinphi
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
+c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
+c &gloc_sc(intertyp,i-3,icg)
+ if (lprn)
+ & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
+ & (v1sccor(j,intertyp,itori,itori1),j=1,6)
+ & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
+ gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
+ enddo !intertyp
+ enddo
+c do i=1,nres
+c write (iout,*) "W@T@F", gloc_sc(1,i,icg),gloc(i,icg)
+c enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine multibody(ecorr)
+C This subroutine calculates multi-body contributions to energy following
+C the idea of Skolnick et al. If side chains I and J make a contact and
+C at the same time side chains I+1 and J+1 make a contact, an extra
+C contribution equal to sqrt(eps(i,j)*eps(i+1,j+1)) is added.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(i2,20(1x,i2,f10.5))')
+ & i,(jcont(j,i),facont(j,i),j=1,num_cont(i))
+ enddo
+ endif
+ ecorr=0.0D0
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+ do i=nnt,nct-2
+
+ DO ISHIFT = 3,4
+
+ i1=i+ishift
+ num_conti=num_cont(i)
+ num_conti1=num_cont(i1)
+ do jj=1,num_conti
+ j=jcont(jj,i)
+ do kk=1,num_conti1
+ j1=jcont(kk,i1)
+ if (j1.eq.j+ishift .or. j1.eq.j-ishift) then
+cd write(iout,*)'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+cd & ' ishift=',ishift
+C Contacts I--J and I+ISHIFT--J+-ISHIFT1 occur simultaneously.
+C The system gains extra energy.
+ ecorr=ecorr+esccorr(i,j,i1,j1,jj,kk)
+ endif ! j1==j+-ishift
+ enddo ! kk
+ enddo ! jj
+
+ ENDDO ! ISHIFT
+
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function esccorr(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+ lprn=.false.
+ eij=facont(jj,i)
+ ekl=facont(kk,k)
+cd write (iout,'(4i5,3f10.5)') i,j,k,l,eij,ekl,-eij*ekl
+C Calculate the multi-body contribution to energy.
+C Calculate multi-body contributions to the gradient.
+cd write (iout,'(2(2i3,3f10.5))')i,j,(gacont(m,jj,i),m=1,3),
+cd & k,l,(gacont(m,kk,k),m=1,3)
+ do m=1,3
+ gx(m) =ekl*gacont(m,jj,i)
+ gx1(m)=eij*gacont(m,kk,k)
+ gradxorr(m,i)=gradxorr(m,i)-gx(m)
+ gradxorr(m,j)=gradxorr(m,j)+gx(m)
+ gradxorr(m,k)=gradxorr(m,k)-gx1(m)
+ gradxorr(m,l)=gradxorr(m,l)+gx1(m)
+ enddo
+ do m=i,j-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+gx(ll)
+ enddo
+ enddo
+ do m=k,l-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+gx1(ll)
+ enddo
+ enddo
+ esccorr=-eij*ekl
+ return
+ end
+c------------------------------------------------------------------------------
+#ifdef MPL
+ subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ integer dimen1,dimen2,atom,indx
+ double precision buffer(dimen1,dimen2)
+ double precision zapas
+ common /contacts_hb/ zapas(3,20,maxres,7),
+ & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
+ & num_cont_hb(maxres),jcont_hb(20,maxres)
+ num_kont=num_cont_hb(atom)
+ do i=1,num_kont
+ do k=1,7
+ do j=1,3
+ buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k)
+ enddo ! j
+ enddo ! k
+ buffer(i,indx+22)=facont_hb(i,atom)
+ buffer(i,indx+23)=ees0p(i,atom)
+ buffer(i,indx+24)=ees0m(i,atom)
+ buffer(i,indx+25)=dfloat(jcont_hb(i,atom))
+ enddo ! i
+ buffer(1,indx+26)=dfloat(num_kont)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ integer dimen1,dimen2,atom,indx
+ double precision buffer(dimen1,dimen2)
+ double precision zapas
+ common /contacts_hb/ zapas(3,20,maxres,7),
+ & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
+ & num_cont_hb(maxres),jcont_hb(20,maxres)
+ num_kont=buffer(1,indx+26)
+ num_kont_old=num_cont_hb(atom)
+ num_cont_hb(atom)=num_kont+num_kont_old
+ do i=1,num_kont
+ ii=i+num_kont_old
+ do k=1,7
+ do j=1,3
+ zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
+ enddo ! j
+ enddo ! k
+ facont_hb(ii,atom)=buffer(i,indx+22)
+ ees0p(ii,atom)=buffer(i,indx+23)
+ ees0m(ii,atom)=buffer(i,indx+24)
+ jcont_hb(ii,atom)=buffer(i,indx+25)
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+#endif
+ subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
+C This subroutine calculates multi-body contributions to hydrogen-bonding
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+#ifdef MPL
+ parameter (max_cont=maxconts)
+ parameter (max_dim=2*(8*3+2))
+ parameter (msglen1=max_cont*max_dim*4)
+ parameter (msglen2=2*msglen1)
+ integer source,CorrelType,CorrelID,Error
+ double precision buffer(max_cont,max_dim)
+#endif
+ double precision gx(3),gx1(3)
+ logical lprn,ldone
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+#ifdef MPL
+ n_corr=0
+ n_corr1=0
+ if (fgProcs.le.1) goto 30
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+C Caution! Following code assumes that electrostatic interactions concerning
+C a given atom are split among at most two processors!
+ CorrelType=477
+ CorrelID=MyID+1
+ ldone=.false.
+ do i=1,max_cont
+ do j=1,max_dim
+ buffer(i,j)=0.0D0
+ enddo
+ enddo
+ mm=mod(MyRank,2)
+cd write (iout,*) 'MyRank',MyRank,' mm',mm
+ if (mm) 20,20,10
+ 10 continue
+cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.gt.0) then
+C Send correlation contributions to the preceding processor
+ msglen=msglen1
+ nn=num_cont_hb(iatel_s)
+ call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
+cd write (iout,*) 'The BUFFER array:'
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
+cd enddo
+ if (ielstart(iatel_s).gt.iatel_s+ispp) then
+ msglen=msglen2
+ call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
+C Clear the contacts of the atom passed to the neighboring processor
+ nn=num_cont_hb(iatel_s+1)
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
+cd enddo
+ num_cont_hb(iatel_s)=0
+ endif
+cd write (iout,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen
+cd write (*,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
+cd write (iout,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+cd write (*,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+ msglen=msglen1
+ endif ! (MyRank.gt.0)
+ if (ldone) goto 30
+ ldone=.true.
+ 20 continue
+cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.lt.fgProcs-1) then
+C Receive correlation contributions from the next processor
+ msglen=msglen1
+ if (ielend(iatel_e).lt.nct-1) msglen=msglen2
+cd write (iout,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+cd write (*,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ nbytes=-1
+ do while (nbytes.le.0)
+ call mp_probe(MyID+1,CorrelType,nbytes)
+ enddo
+cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
+ call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
+cd write (iout,*) 'Processor',MyID,
+cd & ' has received correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' nbytes=',nbytes
+cd write (iout,*) 'The received BUFFER array:'
+cd do i=1,max_cont
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
+cd enddo
+ if (msglen.eq.msglen1) then
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
+ else if (msglen.eq.msglen2) then
+ call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
+ else
+ write (iout,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ write (*,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ call mp_stopall(Error)
+ endif ! msglen.eq.msglen1
+ endif ! MyRank.lt.fgProcs-1
+ if (ldone) goto 30
+ ldone=.true.
+ goto 10
+ 30 continue
+#endif
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+ ecorr=0.0D0
+C Remove the loop below after debugging !!!
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+C Calculate the local-electrostatic correlation terms
+ do i=iatel_s,iatel_e+1
+ i1=i+1
+ num_conti=num_cont_hb(i)
+ num_conti1=num_cont_hb(i+1)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ do kk=1,num_conti1
+ j1=jcont_hb(kk,i1)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1 .or. j1.eq.j-1) then
+C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
+C The system gains extra energy.
+ ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+ n_corr=n_corr+1
+ else if (j1.eq.j) then
+C Contacts I-J and I-(J+1) occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
+ endif
+ enddo ! kk
+ do kk=1,num_conti
+ j1=jcont_hb(kk,i)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1) then
+C Contacts I-J and (I+1)-J occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
+ endif ! j1==j+1
+ enddo ! kk
+ enddo ! jj
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,
+ & n_corr1)
+C This subroutine calculates multi-body contributions to hydrogen-bonding
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+#ifdef MPL
+ parameter (max_cont=maxconts)
+ parameter (max_dim=2*(8*3+2))
+ parameter (msglen1=max_cont*max_dim*4)
+ parameter (msglen2=2*msglen1)
+ integer source,CorrelType,CorrelID,Error
+ double precision buffer(max_cont,max_dim)
+#endif
+ double precision gx(3),gx1(3)
+ logical lprn,ldone
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+ eturn6=0.0d0
+#ifdef MPL
+ n_corr=0
+ n_corr1=0
+ if (fgProcs.le.1) goto 30
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+C Caution! Following code assumes that electrostatic interactions concerning
+C a given atom are split among at most two processors!
+ CorrelType=477
+ CorrelID=MyID+1
+ ldone=.false.
+ do i=1,max_cont
+ do j=1,max_dim
+ buffer(i,j)=0.0D0
+ enddo
+ enddo
+ mm=mod(MyRank,2)
+cd write (iout,*) 'MyRank',MyRank,' mm',mm
+ if (mm) 20,20,10
+ 10 continue
+cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.gt.0) then
+C Send correlation contributions to the preceding processor
+ msglen=msglen1
+ nn=num_cont_hb(iatel_s)
+ call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
+cd write (iout,*) 'The BUFFER array:'
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
+cd enddo
+ if (ielstart(iatel_s).gt.iatel_s+ispp) then
+ msglen=msglen2
+ call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
+C Clear the contacts of the atom passed to the neighboring processor
+ nn=num_cont_hb(iatel_s+1)
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
+cd enddo
+ num_cont_hb(iatel_s)=0
+ endif
+cd write (iout,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen
+cd write (*,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
+cd write (iout,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+cd write (*,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+ msglen=msglen1
+ endif ! (MyRank.gt.0)
+ if (ldone) goto 30
+ ldone=.true.
+ 20 continue
+cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.lt.fgProcs-1) then
+C Receive correlation contributions from the next processor
+ msglen=msglen1
+ if (ielend(iatel_e).lt.nct-1) msglen=msglen2
+cd write (iout,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+cd write (*,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ nbytes=-1
+ do while (nbytes.le.0)
+ call mp_probe(MyID+1,CorrelType,nbytes)
+ enddo
+cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
+ call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
+cd write (iout,*) 'Processor',MyID,
+cd & ' has received correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' nbytes=',nbytes
+cd write (iout,*) 'The received BUFFER array:'
+cd do i=1,max_cont
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
+cd enddo
+ if (msglen.eq.msglen1) then
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
+ else if (msglen.eq.msglen2) then
+ call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
+ else
+ write (iout,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ write (*,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ call mp_stopall(Error)
+ endif ! msglen.eq.msglen1
+ endif ! MyRank.lt.fgProcs-1
+ if (ldone) goto 30
+ ldone=.true.
+ goto 10
+ 30 continue
+#endif
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+ ecorr=0.0D0
+ ecorr5=0.0d0
+ ecorr6=0.0d0
+C Remove the loop below after debugging !!!
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+C Calculate the dipole-dipole interaction energies
+ if (wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) then
+ do i=iatel_s,iatel_e+1
+ num_conti=num_cont_hb(i)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ call dipole(i,j,jj)
+ enddo
+ enddo
+ endif
+C Calculate the local-electrostatic correlation terms
+ do i=iatel_s,iatel_e+1
+ i1=i+1
+ num_conti=num_cont_hb(i)
+ num_conti1=num_cont_hb(i+1)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ do kk=1,num_conti1
+ j1=jcont_hb(kk,i1)
+c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1 .or. j1.eq.j-1) then
+C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
+C The system gains extra energy.
+ n_corr=n_corr+1
+ sqd1=dsqrt(d_cont(jj,i))
+ sqd2=dsqrt(d_cont(kk,i1))
+ sred_geom = sqd1*sqd2
+ IF (sred_geom.lt.cutoff_corr) THEN
+ call gcont(sred_geom,r0_corr,1.0D0,delt_corr,
+ & ekont,fprimcont)
+c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ fac_prim1=0.5d0*sqd2/sqd1*fprimcont
+ fac_prim2=0.5d0*sqd1/sqd2*fprimcont
+ do l=1,3
+ g_contij(l,1)=fac_prim1*grij_hb_cont(l,jj,i)
+ g_contij(l,2)=fac_prim2*grij_hb_cont(l,kk,i1)
+ enddo
+ n_corr1=n_corr1+1
+cd write (iout,*) 'sred_geom=',sred_geom,
+cd & ' ekont=',ekont,' fprim=',fprimcont
+ call calc_eello(i,j,i+1,j1,jj,kk)
+ if (wcorr4.gt.0.0d0)
+ & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk)
+ if (wcorr5.gt.0.0d0)
+ & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk)
+c print *,"wcorr5",ecorr5
+cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6
+cd write(2,*)'ijkl',i,j,i+1,j1
+ if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
+ & .or. wturn6.eq.0.0d0))then
+cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
+ ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
+cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
+cd & 'ecorr6=',ecorr6
+cd write (iout,'(4e15.5)') sred_geom,
+cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
+cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
+cd & dabs(eello6(i,j,i+1,j1,jj,kk))
+ else if (wturn6.gt.0.0d0
+ & .and. (j.eq.i+4 .and. j1.eq.i+3)) then
+cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
+ eturn6=eturn6+eello_turn6(i,jj,kk)
+cd write (2,*) 'multibody_eello:eturn6',eturn6
+ endif
+ ENDIF
+1111 continue
+ else if (j1.eq.j) then
+C Contacts I-J and I-(J+1) occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
+ endif
+ enddo ! kk
+ do kk=1,num_conti
+ j1=jcont_hb(kk,i)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1) then
+C Contacts I-J and (I+1)-J occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
+ endif ! j1==j+1
+ enddo ! kk
+ enddo ! jj
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function ehbcorr(i,j,k,l,jj,kk,coeffp,coeffm)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+ lprn=.false.
+ eij=facont_hb(jj,i)
+ ekl=facont_hb(kk,k)
+ ees0pij=ees0p(jj,i)
+ ees0pkl=ees0p(kk,k)
+ ees0mij=ees0m(jj,i)
+ ees0mkl=ees0m(kk,k)
+ ekont=eij*ekl
+ ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl)
+cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl)
+C Following 4 lines for diagnostics.
+cd ees0pkl=0.0D0
+cd ees0pij=1.0D0
+cd ees0mkl=0.0D0
+cd ees0mij=1.0D0
+c write (iout,*)'Contacts have occurred for peptide groups',i,j,
+c & ' and',k,l
+c write (iout,*)'Contacts have occurred for peptide groups',
+c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
+c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
+C Calculate the multi-body contribution to energy.
+ ecorr=ecorr+ekont*ees
+ if (calc_grad) then
+C Calculate multi-body contributions to the gradient.
+ do ll=1,3
+ ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i)
+ gradcorr(ll,i)=gradcorr(ll,i)+ghalf
+ & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb1(ll,jj,i))
+ gradcorr(ll,j)=gradcorr(ll,j)+ghalf
+ & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb2(ll,jj,i))
+ ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k)
+ gradcorr(ll,k)=gradcorr(ll,k)+ghalf
+ & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb1(ll,kk,k))
+ gradcorr(ll,l)=gradcorr(ll,l)+ghalf
+ & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb2(ll,kk,k))
+ enddo
+ do m=i+1,j-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+
+ & ees*ekl*gacont_hbr(ll,jj,i)-
+ & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+
+ & ees*eij*gacont_hbr(ll,kk,k)-
+ & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
+ enddo
+ enddo
+ endif
+ ehbcorr=ekont*ees
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine dipole(i,j,jj)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ dimension dipi(2,2),dipj(2,2),dipderi(2),dipderj(2),auxvec(2),
+ & auxmat(2,2)
+ iti1 = itortyp(itype(i+1))
+ if (j.lt.nres-1) then
+ itj1 = itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ do iii=1,2
+ dipi(iii,1)=Ub2(iii,i)
+ dipderi(iii)=Ub2der(iii,i)
+ dipi(iii,2)=b1(iii,iti1)
+ dipj(iii,1)=Ub2(iii,j)
+ dipderj(iii)=Ub2der(iii,j)
+ dipj(iii,2)=b1(iii,itj1)
+ enddo
+ kkk=0
+ do iii=1,2
+ call matvec2(a_chuj(1,1,jj,i),dipj(1,iii),auxvec(1))
+ do jjj=1,2
+ kkk=kkk+1
+ dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
+ enddo
+ enddo
+ if (.not.calc_grad) return
+ do kkk=1,5
+ do lll=1,3
+ mmm=0
+ do iii=1,2
+ call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),dipj(1,iii),
+ & auxvec(1))
+ do jjj=1,2
+ mmm=mmm+1
+ dipderx(lll,kkk,mmm,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
+ enddo
+ enddo
+ enddo
+ enddo
+ call transpose2(a_chuj(1,1,jj,i),auxmat(1,1))
+ call matvec2(auxmat(1,1),dipderi(1),auxvec(1))
+ do iii=1,2
+ dipderg(iii,jj,i)=scalar2(auxvec(1),dipj(1,iii))
+ enddo
+ call matvec2(a_chuj(1,1,jj,i),dipderj(1),auxvec(1))
+ do iii=1,2
+ dipderg(iii+2,jj,i)=scalar2(auxvec(1),dipi(1,iii))
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine calc_eello(i,j,k,l,jj,kk)
+C
+C This subroutine computes matrices and vectors needed to calculate
+C the fourth-, fifth-, and sixth-order local-electrostatic terms.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision aa1(2,2),aa2(2,2),aa1t(2,2),aa2t(2,2),
+ & aa1tder(2,2,3,5),aa2tder(2,2,3,5),auxmat(2,2)
+ logical lprn
+ common /kutas/ lprn
+cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l,
+cd & ' jj=',jj,' kk=',kk
+cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return
+ do iii=1,2
+ do jjj=1,2
+ aa1(iii,jjj)=a_chuj(iii,jjj,jj,i)
+ aa2(iii,jjj)=a_chuj(iii,jjj,kk,k)
+ enddo
+ enddo
+ call transpose2(aa1(1,1),aa1t(1,1))
+ call transpose2(aa2(1,1),aa2t(1,1))
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(a_chuj_der(1,1,lll,kkk,jj,i),
+ & aa1tder(1,1,lll,kkk))
+ call transpose2(a_chuj_der(1,1,lll,kkk,kk,k),
+ & aa2tder(1,1,lll,kkk))
+ enddo
+ enddo
+ if (l.eq.j+1) then
+C parallel orientation of the two CA-CA-CA frames.
+ if (i.gt.1) then
+ iti=itortyp(itype(i))
+ else
+ iti=ntortyp+1
+ endif
+ itk1=itortyp(itype(k+1))
+ itj=itortyp(itype(j))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+C A1 kernel(j+1) A2T
+cd do iii=1,2
+cd write (iout,'(3f10.5,5x,3f10.5)')
+cd & (EUg(iii,jjj,k),jjj=1,2),(EUg(iii,jjj,l),jjj=1,2)
+cd enddo
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.false.,EUg(1,1,l),EUgder(1,1,l),
+ & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0) THEN
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.false.,EUgC(1,1,l),EUgCder(1,1,l),
+ & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.false.,Ug2DtEUg(1,1,l),
+ & Ug2DtEUgder(1,1,1,l),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
+ & ADtEAderx(1,1,1,1,1,1))
+ lprn=.false.
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.false.,DtUg2EUg(1,1,l),
+ & DtUg2EUgder(1,1,1,l),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
+ & ADtEA1derx(1,1,1,1,1,1))
+ ENDIF
+C End 6-th order cumulants
+cd lprn=.false.
+cd if (lprn) then
+cd write (2,*) 'In calc_eello6'
+cd do iii=1,2
+cd write (2,*) 'iii=',iii
+cd do kkk=1,5
+cd write (2,*) 'kkk=',kkk
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
+cd enddo
+cd enddo
+cd enddo
+cd endif
+ call transpose2(EUgder(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & EAEAderx(1,1,lll,kkk,iii,1))
+ enddo
+ enddo
+ enddo
+C A1T kernel(i+1) A2
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUg(1,1,k),EUgder(1,1,k),
+ & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0) THEN
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUgC(1,1,k),EUgCder(1,1,k),
+ & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),2,.false.,Ug2DtEUg(1,1,k),
+ & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
+ & ADtEAderx(1,1,1,1,1,2))
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),2,.false.,DtUg2EUg(1,1,k),
+ & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
+ & ADtEA1derx(1,1,1,1,1,2))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,l),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEAderg(1,1,1,2))
+ call transpose2(EUg(1,1,l),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & EAEAderx(1,1,lll,kkk,iii,2))
+ enddo
+ enddo
+ enddo
+C AEAb1 and AEAb2
+C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
+C They are needed only when the fifth- or the sixth-order cumulants are
+C indluded.
+ IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
+ call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
+ call transpose2(AEAderg(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
+ call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
+ call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
+ call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
+ call transpose2(AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
+ call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
+ call transpose2(AEAderg(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
+ call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
+ call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
+ call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
+C Calculate the Cartesian derivatives of the vectors.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),
+ & AEAb1derx(1,lll,kkk,iii,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),
+ & AEAb2derx(1,lll,kkk,iii,1,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & AEAb1derx(1,lll,kkk,iii,2,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
+ & AEAb2derx(1,lll,kkk,iii,2,1))
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),
+ & AEAb1derx(1,lll,kkk,iii,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),
+ & AEAb2derx(1,lll,kkk,iii,1,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ & AEAb1derx(1,lll,kkk,iii,2,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
+ & AEAb2derx(1,lll,kkk,iii,2,2))
+ enddo
+ enddo
+ enddo
+ ENDIF
+C End vectors
+ else
+C Antiparallel orientation of the two CA-CA-CA frames.
+ if (i.gt.1) then
+ iti=itortyp(itype(i))
+ else
+ iti=ntortyp+1
+ endif
+ itk1=itortyp(itype(k+1))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+C A2 kernel(j-1)T A1T
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.true.,EUg(1,1,j),EUgder(1,1,j),
+ & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
+ & j.eq.i+4 .and. l.eq.i+3)) THEN
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.true.,EUgC(1,1,j),EUgCder(1,1,j),
+ & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
+ call kernel(aa2(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.true.,Ug2DtEUg(1,1,j),
+ & Ug2DtEUgder(1,1,1,j),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
+ & ADtEAderx(1,1,1,1,1,1))
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.true.,DtUg2EUg(1,1,j),
+ & DtUg2EUgder(1,1,1,j),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
+ & ADtEA1derx(1,1,1,1,1,1))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & EAEAderx(1,1,lll,kkk,iii,1))
+ enddo
+ enddo
+ enddo
+C A2T kernel(i+1)T A1
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUg(1,1,k),EUgder(1,1,k),
+ & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
+ & j.eq.i+4 .and. l.eq.i+3)) THEN
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUgC(1,1,k),EUgCder(1,1,k),
+ & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),2,.true.,Ug2DtEUg(1,1,k),
+ & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
+ & ADtEAderx(1,1,1,1,1,2))
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),2,.true.,DtUg2EUg(1,1,k),
+ & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
+ & ADtEA1derx(1,1,1,1,1,2))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,j),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,2,2))
+ call transpose2(EUg(1,1,j),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & EAEAderx(1,1,lll,kkk,iii,2))
+ enddo
+ enddo
+ enddo
+C AEAb1 and AEAb2
+C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
+C They are needed only when the fifth- or the sixth-order cumulants are
+C indluded.
+ IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
+ & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
+ call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
+ call transpose2(AEAderg(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
+ call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
+ call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
+ call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
+ call transpose2(AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
+ call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
+ call transpose2(AEAderg(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
+ call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
+ call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
+ call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
+C Calculate the Cartesian derivatives of the vectors.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),
+ & AEAb1derx(1,lll,kkk,iii,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),
+ & AEAb2derx(1,lll,kkk,iii,1,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & AEAb1derx(1,lll,kkk,iii,2,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
+ & AEAb2derx(1,lll,kkk,iii,2,1))
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itl),
+ & AEAb1derx(1,lll,kkk,iii,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),
+ & AEAb2derx(1,lll,kkk,iii,1,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
+ & AEAb1derx(1,lll,kkk,iii,2,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
+ & AEAb2derx(1,lll,kkk,iii,2,2))
+ enddo
+ enddo
+ enddo
+ ENDIF
+C End vectors
+ endif
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine kernel(aa1,aa2t,aa1derx,aa2tderx,nderg,transp,
+ & KK,KKderg,AKA,AKAderg,AKAderx)
+ implicit none
+ integer nderg
+ logical transp
+ double precision aa1(2,2),aa2t(2,2),aa1derx(2,2,3,5),
+ & aa2tderx(2,2,3,5),KK(2,2),KKderg(2,2,nderg),AKA(2,2),
+ & AKAderg(2,2,nderg),AKAderx(2,2,3,5,2)
+ integer iii,kkk,lll
+ integer jjj,mmm
+ logical lprn
+ common /kutas/ lprn
+ call prodmat3(aa1(1,1),aa2t(1,1),KK(1,1),transp,AKA(1,1))
+ do iii=1,nderg
+ call prodmat3(aa1(1,1),aa2t(1,1),KKderg(1,1,iii),transp,
+ & AKAderg(1,1,iii))
+ enddo
+cd if (lprn) write (2,*) 'In kernel'
+ do kkk=1,5
+cd if (lprn) write (2,*) 'kkk=',kkk
+ do lll=1,3
+ call prodmat3(aa1derx(1,1,lll,kkk),aa2t(1,1),
+ & KK(1,1),transp,AKAderx(1,1,lll,kkk,1))
+cd if (lprn) then
+cd write (2,*) 'lll=',lll
+cd write (2,*) 'iii=1'
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & (AKAderx(jjj,mmm,lll,kkk,1),mmm=1,2)
+cd enddo
+cd endif
+ call prodmat3(aa1(1,1),aa2tderx(1,1,lll,kkk),
+ & KK(1,1),transp,AKAderx(1,1,lll,kkk,2))
+cd if (lprn) then
+cd write (2,*) 'lll=',lll
+cd write (2,*) 'iii=2'
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & (AKAderx(jjj,mmm,lll,kkk,2),mmm=1,2)
+cd enddo
+cd endif
+ enddo
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ double precision function eello4(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision pizda(2,2),ggg1(3),ggg2(3)
+cd if (i.ne.1 .or. j.ne.5 .or. k.ne.2 .or.l.ne.4) then
+cd eello4=0.0d0
+cd return
+cd endif
+cd print *,'eello4:',i,j,k,l,jj,kk
+cd write (2,*) 'i',i,' j',j,' k',k,' l',l
+cd call checkint4(i,j,k,l,jj,kk,eel4_num)
+cold eij=facont_hb(jj,i)
+cold ekl=facont_hb(kk,k)
+cold ekont=eij*ekl
+ eel4=-EAEA(1,1,1)-EAEA(2,2,1)
+ if (calc_grad) then
+cd eel41=-EAEA(1,1,2)-EAEA(2,2,2)
+ gcorr_loc(k-1)=gcorr_loc(k-1)
+ & -ekont*(EAEAderg(1,1,1,1)+EAEAderg(2,2,1,1))
+ if (l.eq.j+1) then
+ gcorr_loc(l-1)=gcorr_loc(l-1)
+ & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+ else
+ gcorr_loc(j-1)=gcorr_loc(j-1)
+ & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+ endif
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=-EAEAderx(1,1,lll,kkk,iii,1)
+ & -EAEAderx(2,2,lll,kkk,iii,1)
+cd derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd gcorr_loc(l-1)=0.0d0
+cd gcorr_loc(j-1)=0.0d0
+cd gcorr_loc(k-1)=0.0d0
+cd eel4=1.0d0
+cd write (iout,*)'Contacts have occurred for peptide groups',
+cd & i,j,' fcont:',eij,' eij',' and ',k,l,
+cd & ' fcont ',ekl,' eel4=',eel4,' eel4_num',16*eel4_num
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i)
+ ggg1(ll)=eel4*g_contij(ll,1)
+ ggg2(ll)=eel4*g_contij(ll,2)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1)
+cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i)
+ gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k)
+ gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,gcorr_loc(iii)
+cd enddo
+ endif
+ eello4=ekont*eel4
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello4',ekont*eel4
+ return
+ end
+C---------------------------------------------------------------------------
+ double precision function eello5(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision pizda(2,2),auxmat(2,2),auxmat1(2,2),vv(2)
+ double precision ggg1(3),ggg2(3)
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel chains C
+C C
+C o o o o C
+C /l\ / \ \ / \ / \ / C
+C / \ / \ \ / \ / \ / C
+C j| o |l1 | o | o| o | | o |o C
+C \ |/k\| |/ \| / |/ \| |/ \| C
+C \i/ \ / \ / / \ / \ C
+C o k1 o C
+C (I) (II) (III) (IV) C
+C C
+C eello5_1 eello5_2 eello5_3 eello5_4 C
+C C
+C Antiparallel chains C
+C C
+C o o o o C
+C /j\ / \ \ / \ / \ / C
+C / \ / \ \ / \ / \ / C
+C j1| o |l | o | o| o | | o |o C
+C \ |/k\| |/ \| / |/ \| |/ \| C
+C \i/ \ / \ / / \ / \ C
+C o k1 o C
+C (I) (II) (III) (IV) C
+C C
+C eello5_1 eello5_2 eello5_3 eello5_4 C
+C C
+C o denotes a local interaction, vertical lines an electrostatic interaction. C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd if (i.ne.2 .or. j.ne.6 .or. k.ne.3 .or. l.ne.5) then
+cd eello5=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+ itk=itortyp(itype(k))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+ eello5_1=0.0d0
+ eello5_2=0.0d0
+ eello5_3=0.0d0
+ eello5_4=0.0d0
+cd call checkint5(i,j,k,l,jj,kk,eel5_1_num,eel5_2_num,
+cd & eel5_3_num,eel5_4_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=facont_hb(jj,i)
+cd ekl=facont_hb(kk,k)
+cd ekont=eij*ekl
+cd write (iout,*)'Contacts have occurred for peptide groups',
+cd & i,j,' fcont:',eij,' eij',' and ',k,l
+cd goto 1111
+C Contribution from the graph I.
+cd write (2,*) 'AEA ',AEA(1,1,1),AEA(2,1,1),AEA(1,2,1),AEA(2,2,1)
+cd write (2,*) 'AEAb2',AEAb2(1,1,1),AEAb2(2,1,1)
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,i)))
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(AEA(1,1,1),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2(1,1,1),Ub2der(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ call matmat2(AEAderg(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ if (l.eq.j+1) then
+ if (l.lt.nres-1) g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ else
+ if (j.lt.nres-1) g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ endif
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
+ enddo
+ enddo
+ enddo
+c goto 1112
+ endif
+c1111 continue
+C Contribution from graph II
+ call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,k))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ if (l.eq.j+1) then
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
+ else
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
+ endif
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+cd1111 continue
+ if (l.eq.j+1) then
+cd goto 1110
+C Parallel orientation
+C Contribution from graph III
+ call transpose2(EUg(1,1,l),auxmat(1,1))
+ call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,j)))
+ call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
+ call transpose2(EUgder(1,1,l),auxmat1(1,1))
+ call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+C Contribution from graph IV
+cd1110 continue
+ call transpose2(EE(1,1,itl),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l))
+ enddo
+ enddo
+ enddo
+ endif
+ else
+C Antiparallel orientation
+C Contribution from graph III
+c goto 1110
+ call transpose2(EUg(1,1,j),auxmat(1,1))
+ call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,l)))
+ call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
+ call transpose2(EUgder(1,1,j),auxmat1(1,1))
+ call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+C Contribution from graph IV
+1110 continue
+ call transpose2(EE(1,1,itj),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,j))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j))
+ enddo
+ enddo
+ enddo
+ endif
+ endif
+1112 continue
+ eel5=eello5_1+eello5_2+eello5_3+eello5_4
+cd if (i.eq.2 .and. j.eq.8 .and. k.eq.3 .and. l.eq.7) then
+cd write (2,*) 'ijkl',i,j,k,l
+cd write (2,*) 'eello5_1',eello5_1,' eello5_2',eello5_2,
+cd & ' eello5_3',eello5_3,' eello5_4',eello5_4
+cd endif
+cd write(iout,*) 'eello5_1',eello5_1,' eel5_1_num',16*eel5_1_num
+cd write(iout,*) 'eello5_2',eello5_2,' eel5_2_num',16*eel5_2_num
+cd write(iout,*) 'eello5_3',eello5_3,' eel5_3_num',16*eel5_3_num
+cd write(iout,*) 'eello5_4',eello5_4,' eel5_4_num',16*eel5_4_num
+ if (calc_grad) then
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont
+ do ll=1,3
+ ggg1(ll)=eel5*g_contij(ll,1)
+ ggg2(ll)=eel5*g_contij(ll,2)
+cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1)
+cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i)
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k)
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
+ enddo
+ enddo
+c1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr5_loc(iii)
+cd enddo
+ endif
+ eello5=ekont*eel5
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello5',ekont*eel5
+ return
+ end
+c--------------------------------------------------------------------------
+ double precision function eello6(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision ggg1(3),ggg2(3)
+cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
+cd eello6=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+ eello6_1=0.0d0
+ eello6_2=0.0d0
+ eello6_3=0.0d0
+ eello6_4=0.0d0
+ eello6_5=0.0d0
+ eello6_6=0.0d0
+cd call checkint6(i,j,k,l,jj,kk,eel6_1_num,eel6_2_num,
+cd & eel6_3_num,eel6_4_num,eel6_5_num,eel6_6_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=facont_hb(jj,i)
+cd ekl=facont_hb(kk,k)
+cd ekont=eij*ekl
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+ if (l.eq.j+1) then
+ eello6_1=eello6_graph1(i,j,k,l,1,.false.)
+ eello6_2=eello6_graph1(j,i,l,k,2,.false.)
+ eello6_3=eello6_graph2(i,j,k,l,jj,kk,.false.)
+ eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
+ eello6_5=eello6_graph4(j,i,l,k,jj,kk,2,.false.)
+ eello6_6=eello6_graph3(i,j,k,l,jj,kk,.false.)
+ else
+ eello6_1=eello6_graph1(i,j,k,l,1,.false.)
+ eello6_2=eello6_graph1(l,k,j,i,2,.true.)
+ eello6_3=eello6_graph2(i,l,k,j,jj,kk,.true.)
+ eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
+ if (wturn6.eq.0.0d0 .or. j.ne.i+4) then
+ eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
+ else
+ eello6_5=0.0d0
+ endif
+ eello6_6=eello6_graph3(i,l,k,j,jj,kk,.true.)
+ endif
+C If turn contributions are considered, they will be handled separately.
+ eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6
+cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num
+cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num
+cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num
+cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num
+cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num
+cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num
+cd goto 1112
+ if (calc_grad) then
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+ ggg1(ll)=eel6*g_contij(ll,1)
+ ggg2(ll)=eel6*g_contij(ll,2)
+cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1)
+ ghalf=0.5d0*ggg2(ll)
+cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k)
+cd ghalf=0.0d0
+ gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i)
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k)
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr6_loc(iii)
+cd enddo
+ endif
+ eello6=ekont*eel6
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello6',ekont*eel6
+ return
+ end
+c--------------------------------------------------------------------------
+ double precision function eello6_graph1(i,j,k,l,imat,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vv(2),vv1(2),pizda(2,2),auxmat(2,2),pizda1(2,2)
+ logical swap
+ logical lprn
+ common /kutas/ lprn
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel Antiparallel C
+C C
+C o o C
+C /l\ /j\ C
+C / \ / \ C
+C /| o | | o |\ C
+C \ j|/k\| / \ |/k\|l / C
+C \ / \ / \ / \ / C
+C o o o o C
+C i i C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+ itk=itortyp(itype(k))
+ s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
+ s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
+ s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
+ call transpose2(EUgC(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
+ vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
+ vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
+ s5=scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
+ eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
+ if (.not. calc_grad) return
+ if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1)
+ & -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i))
+ & -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,2,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2der(1,i))
+ & +scalar2(vv(1),Dtobr2der(1,i)))
+ call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
+ vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
+ if (l.eq.j+1) then
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)
+ & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
+ & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)
+ & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
+ & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
+ endif
+ call transpose2(EUgCder(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ if (k.gt.1) g_corr6_loc(k-1)=g_corr6_loc(k-1)
+ & +ekont*(-0.5d0*(-scalar2(AEAb2(1,1,imat),Ug2Db1tder(1,k))
+ & +scalar2(AEAb2(1,1,imat),CUgb2der(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))))
+ do iii=1,2
+ if (swap) then
+ ind=3-iii
+ else
+ ind=iii
+ endif
+ do kkk=1,5
+ do lll=1,3
+ s1= scalar2(AEAb1derx(1,lll,kkk,iii,2,imat),CUgb2(1,i))
+ s2=-scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),Ug2Db1t(1,k))
+ s3= scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),CUgb2(1,k))
+ call transpose2(EUgC(1,1,k),auxmat(1,1))
+ call matmat2(AEAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
+ & pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
+ vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
+ & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
+ vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
+ & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
+ s5=scalar2(vv(1),Dtobr2(1,i))
+ derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph2(i,j,k,l,jj,kk,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ logical swap
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
+ & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ logical lprn
+ common /kutas/ lprn
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel Antiparallel C
+C C
+C o o C
+C \ /l\ /j\ / C
+C \ / \ / \ / C
+C o| o | | o |o C
+C \ j|/k\| \ |/k\|l C
+C \ / \ \ / \ C
+C o o C
+C i i C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
+C AL 7/4/01 s1 would occur in the sixth-order moment,
+C but not in a cluster cumulant
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dip(1,kk,k)
+#endif
+ call matvec2(ADtEA1(1,1,1),Ub2(1,k),auxvec(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matvec2(ADtEA(1,1,2),Ub2(1,l),auxvec1(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec1(1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(ADtEA1(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 'eello6_graph2:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph2=-(s1+s2+s3+s4)
+#else
+ eello6_graph2=-(s2+s3+s4)
+#endif
+c eello6_graph2=-s3
+ if (.not. calc_grad) return
+C Derivatives in gamma(i-1)
+ if (i.gt.1) then
+#ifdef MOMENT
+ s1=dipderg(1,jj,i)*dip(1,kk,k)
+#endif
+ s2=-0.5d0*scalar2(Ub2der(1,i),auxvec(1))
+ call matvec2(ADtEAderg(1,1,1,2),Ub2(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ s4=-0.25d0*scalar2(vv(1),Dtobr2der(1,i))
+#ifdef MOMENT
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
+#endif
+c g_corr6_loc(i-1)=g_corr6_loc(i-1)-s3
+ endif
+C Derivatives in gamma(k-1)
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dipderg(1,kk,k)
+#endif
+ call matvec2(ADtEA1(1,1,1),Ub2der(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ call matvec2(ADtEAderg(1,1,2,2),Ub2(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(ADtEA1(1,1,1),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
+#endif
+c g_corr6_loc(k-1)=g_corr6_loc(k-1)-s3
+C Derivatives in gamma(j-1) or gamma(l-1)
+ if (j.gt.1) then
+#ifdef MOMENT
+ s1=dipderg(3,jj,i)*dip(1,kk,k)
+#endif
+ call matvec2(ADtEA1derg(1,1,1,1),Ub2(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2der(1,j),auxvec1(1))
+ call matmat2(ADtEA1derg(1,1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ if (swap) then
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
+ endif
+#endif
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s3+s4)
+c g_corr6_loc(j-1)=g_corr6_loc(j-1)-s3
+ endif
+C Derivatives in gamma(l-1) or gamma(j-1)
+ if (l.gt.1) then
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dipderg(3,kk,k)
+#endif
+ call matvec2(ADtEA1derg(1,1,2,1),Ub2(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ call matvec2(ADtEA(1,1,2),Ub2der(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ call matmat2(ADtEA1derg(1,1,2,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ if (swap) then
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
+ else
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
+ endif
+#endif
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s3+s4)
+c g_corr6_loc(l-1)=g_corr6_loc(l-1)-s3
+ endif
+C Cartesian derivatives.
+ if (lprn) then
+ write (2,*) 'In eello6_graph2'
+ do iii=1,2
+ write (2,*) 'iii=',iii
+ do kkk=1,5
+ write (2,*) 'kkk=',kkk
+ do jjj=1,2
+ write (2,'(3(2f10.5),5x)')
+ & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
+ enddo
+ enddo
+ enddo
+ endif
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ s1=dipderx(lll,kkk,1,jj,i)*dip(1,kk,k)
+ else
+ s1=dip(1,jj,i)*dipderx(lll,kkk,1,kk,k)
+ endif
+#endif
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,1),Ub2(1,k),
+ & auxvec(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matvec2(ADtEAderx(1,1,lll,kkk,iii,2),Ub2(1,l),
+ & auxvec(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec(1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(ADtEA1derx(1,1,lll,kkk,iii,1),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (swap) then
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph3(i,j,k,l,jj,kk,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
+ logical swap
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel Antiparallel C
+C C
+C o o C
+C /l\ / \ /j\ C
+C / \ / \ / \ C
+C /| o |o o| o |\ C
+C j|/k\| / |/k\|l / C
+C / \ / / \ / C
+C / o / o C
+C i i C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C 4/7/01 AL Component s1 was removed, because it pertains to the respective
+C energy moment and not to the cluster cumulant.
+ iti=itortyp(itype(i))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ itk=itortyp(itype(k))
+ itk1=itortyp(itype(k+1))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+#ifdef MOMENT
+ s1=dip(4,jj,i)*dip(4,kk,k)
+#endif
+ call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph3=-(s1+s2+s3+s4)
+#else
+ eello6_graph3=-(s2+s3+s4)
+#endif
+c eello6_graph3=-s4
+ if (.not. calc_grad) return
+C Derivatives in gamma(k-1)
+ call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
+C Derivatives in gamma(l-1)
+ call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
+C Cartesian derivatives.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ s1=dipderx(lll,kkk,4,jj,i)*dip(4,kk,k)
+ else
+ s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
+ endif
+#endif
+ call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ & auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (swap) then
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+c derx(lll,kkk,iii)=derx(lll,kkk,iii)-s4
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
+ & auxvec1(2),auxmat1(2,2)
+ logical swap
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel Antiparallel C
+C C
+C o o C
+C /l\ / \ /j\ C
+C / \ / \ / \ C
+C /| o |o o| o |\ C
+C \ j|/k\| \ |/k\|l C
+C \ / \ \ / \ C
+C o \ o \ C
+C i i C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C 4/7/01 AL Component s1 was removed, because it pertains to the respective
+C energy moment and not to the cluster cumulant.
+cd write (2,*) 'eello_graph4: wturn6',wturn6
+ iti=itortyp(itype(i))
+ itj=itortyp(itype(j))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ itk=itortyp(itype(k))
+ if (k.lt.nres-1) then
+ itk1=itortyp(itype(k+1))
+ else
+ itk1=ntortyp+1
+ endif
+ itl=itortyp(itype(l))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
+cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
+cd & ' itl',itl,' itl1',itl1
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dip(3,kk,k)
+ else
+ s1=dip(2,jj,j)*dip(2,kk,l)
+ endif
+#endif
+ call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 'eello6_graph4:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph4=-(s1+s2+s3+s4)
+#else
+ eello6_graph4=-(s2+s3+s4)
+#endif
+ if (.not. calc_grad) return
+C Derivatives in gamma(i-1)
+ if (i.gt.1) then
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dipderg(2,jj,i)*dip(3,kk,k)
+ else
+ s1=dipderg(4,jj,j)*dip(2,kk,l)
+ endif
+#endif
+ s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+cd write (2,*) 'turn6 derivatives'
+#ifdef MOMENT
+ gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s2+s3+s4)
+#endif
+ else
+#ifdef MOMENT
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
+#endif
+ endif
+ endif
+C Derivatives in gamma(k-1)
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dipderg(2,kk,k)
+ else
+ s1=dip(2,jj,j)*dipderg(4,kk,l)
+ endif
+#endif
+ call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+#ifdef MOMENT
+ gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s2+s3+s4)
+#endif
+ else
+#ifdef MOMENT
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
+#endif
+ endif
+C Derivatives in gamma(j-1) or gamma(l-1)
+ if (l.eq.j+1 .and. l.gt.1) then
+ call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
+ else if (j.gt.1) then
+ call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+ gel_loc_turn6(j-1)=gel_loc_turn6(j-1)-ekont*(s2+s4)
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s4)
+ endif
+ endif
+C Cartesian derivatives.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ if (imat.eq.1) then
+ s1=dipderx(lll,kkk,3,jj,i)*dip(3,kk,k)
+ else
+ s1=dipderx(lll,kkk,2,jj,j)*dip(2,kk,l)
+ endif
+ else
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dipderx(lll,kkk,3,kk,k)
+ else
+ s1=dip(2,jj,j)*dipderx(lll,kkk,2,kk,l)
+ endif
+ endif
+#endif
+ call matvec2(AECAderx(1,1,lll,kkk,iii,imat),Ub2(1,k),
+ & auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
+ & b1(1,itj1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
+ else
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
+ & b1(1,itl1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
+ endif
+ call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (swap) then
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+#ifdef MOMENT
+ derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
+ & -(s1+s2+s4)
+#else
+ derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
+ & -(s2+s4)
+#endif
+ derx_turn(lll,kkk,iii)=derx_turn(lll,kkk,iii)-s3
+ else
+#ifdef MOMENT
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s2+s4)
+#endif
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+ else
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (l.eq.j+1) then
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ else
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ endif
+ endif
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello_turn6(i,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vtemp1(2),vtemp2(2),vtemp3(2),vtemp4(2),
+ & atemp(2,2),auxmat(2,2),achuj_temp(2,2),gtemp(2,2),gvec(2),
+ & ggg1(3),ggg2(3)
+ double precision vtemp1d(2),vtemp2d(2),vtemp3d(2),vtemp4d(2),
+ & atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2)
+C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to
+C the respective energy moment and not to the cluster cumulant.
+ eello_turn6=0.0d0
+ j=i+4
+ k=i+1
+ l=i+3
+ iti=itortyp(itype(i))
+ itk=itortyp(itype(k))
+ itk1=itortyp(itype(k+1))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
+cd write (2,*) 'i',i,' k',k,' j',j,' l',l
+cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
+cd eello6=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+cd call checkint_turn6(i,jj,kk,eel_turn6_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx_turn(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+ eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
+cd eello6_5=0.0d0
+cd write (2,*) 'eello6_5',eello6_5
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
+ ss1=scalar2(Ub2(1,i+2),b1(1,itl))
+ s1 = (auxmat(1,1)+auxmat(2,2))*ss1
+#else
+ s1 = 0.0d0
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
+ s2 = scalar2(b1(1,itk),vtemp1(1))
+#ifdef MOMENT
+ call transpose2(AEA(1,1,2),atemp(1,1))
+ call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
+ call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
+ s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#else
+ s8=0.0d0
+#endif
+ call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
+ s12 = scalar2(Ub2(1,i+2),vtemp3(1))
+#ifdef MOMENT
+ call transpose2(a_chuj(1,1,kk,i+1),achuj_temp(1,1))
+ call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
+ call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
+ call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
+ ss13 = scalar2(b1(1,itk),vtemp4(1))
+ s13 = (gtemp(1,1)+gtemp(2,2))*ss13
+#else
+ s13=0.0d0
+#endif
+c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
+c s1=0.0d0
+c s2=0.0d0
+c s8=0.0d0
+c s12=0.0d0
+c s13=0.0d0
+ eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13)
+ if (calc_grad) then
+C Derivatives in gamma(i+2)
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmatd(1,1))
+ call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+ call transpose2(AEAderg(1,1,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#else
+ s8d=0.0d0
+#endif
+ call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+ gel_loc_turn6(i)=gel_loc_turn6(i)-0.5d0*ekont*(s1d+s8d+s12d)
+C Derivatives in gamma(i+3)
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
+#else
+ s1d=0.0d0
+#endif
+ call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
+ s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
+#endif
+ s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
+#ifdef MOMENT
+ call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
+ s13d = (gtempd(1,1)+gtempd(2,2))*ss13
+#else
+ s13d=0.0d0
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
+ & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
+#else
+ gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
+ & -0.5d0*ekont*(s2d+s12d)
+#endif
+C Derivatives in gamma(i+4)
+ call matmat2(EUgder(1,1,i+3),AEA(1,1,2),auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+#ifdef MOMENT
+ call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1))
+ s13d = (gtempd(1,1)+gtempd(2,2))*ss13
+#else
+ s13d = 0.0d0
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+C s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d+s13d)
+#else
+ gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d)
+#endif
+C Derivatives in gamma(i+5)
+#ifdef MOMENT
+ call transpose2(AEAderg(1,1,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+#else
+ s1d = 0.0d0
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call transpose2(AEA(1,1,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#else
+ s8d = 0.0d0
+#endif
+ call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+#ifdef MOMENT
+ call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
+ ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
+#else
+ s13d = 0.0d0
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
+ & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
+#else
+ gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
+ & -0.5d0*ekont*(s2d+s12d)
+#endif
+C Cartesian derivatives
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+#else
+ s1d = 0.0d0
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
+ & vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*
+ & scalar2(cc(1,1,itl),vtemp2(1))
+#else
+ s8d = 0.0d0
+#endif
+ call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
+ & auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
+ & - 0.5d0*(s1d+s2d)
+#else
+ derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
+ & - 0.5d0*s2d
+#endif
+#ifdef MOMENT
+ derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
+ & - 0.5d0*(s8d+s12d)
+#else
+ derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
+ & - 0.5d0*s12d
+#endif
+ enddo
+ enddo
+ enddo
+#ifdef MOMENT
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(a_chuj_der(1,1,lll,kkk,kk,i+1),
+ & achuj_tempd(1,1))
+ call matmat2(achuj_tempd(1,1),EUg(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
+ s13d=(gtempd(1,1)+gtempd(2,2))*ss13
+ derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
+ call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
+ & vtemp4d(1))
+ ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
+ derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
+ enddo
+ enddo
+#endif
+cd write(iout,*) 'eel6_turn6',eel_turn6,' eel_turn6_num',
+cd & 16*eel_turn6_num
+cd goto 1112
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+ ggg1(ll)=eel_turn6*g_contij(ll,1)
+ ggg2(ll)=eel_turn6*g_contij(ll,2)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf
+ & +ekont*derx_turn(ll,2,1)
+ gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1)
+ gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf
+ & +ekont*derx_turn(ll,4,1)
+ gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf
+ & +ekont*derx_turn(ll,2,2)
+ gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2)
+ gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf
+ & +ekont*derx_turn(ll,4,2)
+ gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr6_loc(iii)
+cd enddo
+ endif
+ eello_turn6=ekont*eel_turn6
+cd write (2,*) 'ekont',ekont
+cd write (2,*) 'eel_turn6',ekont*eel_turn6
+ return
+ end
+crc-------------------------------------------------
+ SUBROUTINE MATVEC2(A1,V1,V2)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ DIMENSION A1(2,2),V1(2),V2(2)
+c DO 1 I=1,2
+c VI=0.0
+c DO 3 K=1,2
+c 3 VI=VI+A1(I,K)*V1(K)
+c Vaux(I)=VI
+c 1 CONTINUE
+
+ vaux1=a1(1,1)*v1(1)+a1(1,2)*v1(2)
+ vaux2=a1(2,1)*v1(1)+a1(2,2)*v1(2)
+
+ v2(1)=vaux1
+ v2(2)=vaux2
+ END
+C---------------------------------------
+ SUBROUTINE MATMAT2(A1,A2,A3)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ DIMENSION A1(2,2),A2(2,2),A3(2,2)
+c DIMENSION AI3(2,2)
+c DO J=1,2
+c A3IJ=0.0
+c DO K=1,2
+c A3IJ=A3IJ+A1(I,K)*A2(K,J)
+c enddo
+c A3(I,J)=A3IJ
+c enddo
+c enddo
+
+ ai3_11=a1(1,1)*a2(1,1)+a1(1,2)*a2(2,1)
+ ai3_12=a1(1,1)*a2(1,2)+a1(1,2)*a2(2,2)
+ ai3_21=a1(2,1)*a2(1,1)+a1(2,2)*a2(2,1)
+ ai3_22=a1(2,1)*a2(1,2)+a1(2,2)*a2(2,2)
+
+ A3(1,1)=AI3_11
+ A3(2,1)=AI3_21
+ A3(1,2)=AI3_12
+ A3(2,2)=AI3_22
+ END
+
+c-------------------------------------------------------------------------
+ double precision function scalar2(u,v)
+ implicit none
+ double precision u(2),v(2)
+ double precision sc
+ integer i
+ scalar2=u(1)*v(1)+u(2)*v(2)
+ return
+ end
+
+C-----------------------------------------------------------------------------
+
+ subroutine transpose2(a,at)
+ implicit none
+ double precision a(2,2),at(2,2)
+ at(1,1)=a(1,1)
+ at(1,2)=a(2,1)
+ at(2,1)=a(1,2)
+ at(2,2)=a(2,2)
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine transpose(n,a,at)
+ implicit none
+ integer n,i,j
+ double precision a(n,n),at(n,n)
+ do i=1,n
+ do j=1,n
+ at(j,i)=a(i,j)
+ enddo
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine prodmat3(a1,a2,kk,transp,prod)
+ implicit none
+ integer i,j
+ double precision a1(2,2),a2(2,2),a2t(2,2),kk(2,2),prod(2,2)
+ logical transp
+crc double precision auxmat(2,2),prod_(2,2)
+
+ if (transp) then
+crc call transpose2(kk(1,1),auxmat(1,1))
+crc call matmat2(a1(1,1),auxmat(1,1),auxmat(1,1))
+crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
+
+ prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,1)
+ & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,1)
+ prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,2)
+ & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,2)
+ prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,1)
+ & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,1)
+ prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,2)
+ & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,2)
+
+ else
+crc call matmat2(a1(1,1),kk(1,1),auxmat(1,1))
+crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
+
+ prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,1)
+ & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,1)
+ prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,2)
+ & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,2)
+ prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,1)
+ & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,1)
+ prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,2)
+ & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,2)
+
+ endif
+c call transpose2(a2(1,1),a2t(1,1))
+
+crc print *,transp
+crc print *,((prod_(i,j),i=1,2),j=1,2)
+crc print *,((prod(i,j),i=1,2),j=1,2)
+
+ return
+ end
+C-----------------------------------------------------------------------------
+ double precision function scalar(u,v)
+ implicit none
+ double precision u(3),v(3)
+ double precision sc
+ integer i
+ sc=0.0d0
+ do i=1,3
+ sc=sc+u(i)*v(i)
+ enddo
+ scalar=sc
+ return
+ end
+
--- /dev/null
+ subroutine etotal(energia)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+
+ external proc_proc
+#ifdef WINPGI
+cMS$ATTRIBUTES C :: proc_proc
+#endif
+
+ include 'COMMON.IOUNITS'
+ double precision energia(0:max_ene),energia1(0:max_ene+1)
+#ifdef MPL
+ include 'COMMON.INFO'
+ external d_vadd
+ integer ready
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot
+cd print *,'nnt=',nnt,' nct=',nct
+C
+C Compute the side-chain and electrostatic interaction energy
+C
+ goto (101,102,103,104,105) ipot
+C Lennard-Jones potential.
+ 101 call elj(evdw)
+cd print '(a)','Exit ELJ'
+ goto 106
+C Lennard-Jones-Kihara potential (shifted).
+ 102 call eljk(evdw)
+ goto 106
+C Berne-Pechukas potential (dilated LJ, angular dependence).
+ 103 call ebp(evdw)
+ goto 106
+C Gay-Berne potential (shifted LJ, angular dependence).
+ 104 call egb(evdw)
+ goto 106
+C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
+ 105 call egbv(evdw)
+C
+C Calculate electrostatic (H-bonding) energy of the main chain.
+C
+ 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
+C
+C Calculate excluded-volume interaction energy between peptide groups
+C and side chains.
+C
+ call escp(evdw2,evdw2_14)
+C
+C Calculate the disulfide-bridge and other energy and the contributions
+C from other distance constraints.
+cd print *,'Calling EHPB'
+ call edis(ehpb)
+cd print *,'EHPB exitted succesfully.'
+C
+C Calculate the virtual-bond-angle energy.
+C
+ call ebend(ebe)
+cd print *,'Bend energy finished.'
+C
+C Calculate the SC local energy.
+C
+ call esc(escloc)
+cd print *,'SCLOC energy finished.'
+C
+C Calculate the virtual-bond torsional energy.
+C
+cd print *,'nterm=',nterm
+ call etor(etors,edihcnstr)
+C
+C 6/23/01 Calculate double-torsional energy
+C
+ call etor_d(etors_d)
+C
+C 12/1/95 Multi-body terms
+C
+ n_corr=0
+ n_corr1=0
+ if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0
+ & .or. wturn6.gt.0.0d0) then
+c print *,"calling multibody_eello"
+ call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
+c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
+c print *,ecorr,ecorr5,ecorr6,eturn6
+ endif
+ if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then
+ call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
+ endif
+C call multibody(ecorr)
+C
+C Sum the energies
+C
+C scale large componenets
+#ifdef SCALE
+ ecorr5_scal=1000.0
+ eel_loc_scal=100.0
+ eello_turn3_scal=100.0
+ eello_turn4_scal=100.0
+ eturn6_scal=1000.0
+ ecorr6_scal=1000.0
+#else
+ ecorr5_scal=1.0
+ eel_loc_scal=1.0
+ eello_turn3_scal=1.0
+ eello_turn4_scal=1.0
+ eturn6_scal=1.0
+ ecorr6_scal=1.0
+#endif
+
+ ecorr5=ecorr5/ecorr5_scal
+ eel_loc=eel_loc/eel_loc_scal
+ eello_turn3=eello_turn3/eello_turn3_scal
+ eello_turn4=eello_turn4/eello_turn4_scal
+ eturn6=eturn6/eturn6_scal
+ ecorr6=ecorr6/ecorr6_scal
+#ifdef MPL
+ if (fgprocs.gt.1) then
+cd call enerprint(evdw,evdw1,evdw2,ees,ebe,escloc,etors,ehpb,
+cd & edihcnstr,ecorr,eel_loc,eello_turn4,etot)
+ energia(1)=evdw
+ energia(2)=evdw2
+ energia(3)=ees
+ energia(4)=evdw1
+ energia(5)=ecorr
+ energia(6)=etors
+ energia(7)=ebe
+ energia(8)=escloc
+ energia(9)=ehpb
+ energia(10)=edihcnstr
+ energia(11)=eel_loc
+ energia(12)=ecorr5
+ energia(13)=ecorr6
+ energia(14)=eello_turn3
+ energia(15)=eello_turn4
+ energia(16)=eturn6
+ energia(17)=etors_d
+ msglen=80
+ do i=1,15
+ energia1(i)=energia(i)
+ enddo
+cd write (iout,*) 'BossID=',BossID,' MyGroup=',MyGroup
+cd write (*,*) 'BossID=',BossID,' MyGroup=',MyGroup
+cd write (*,*) 'Processor',MyID,' calls MP_REDUCE in ENERGY',
+cd & ' BossID=',BossID,' MyGroup=',MyGroup
+ call mp_reduce(energia1(1),energia(1),msglen,BossID,d_vadd,
+ & fgGroupID)
+cd write (iout,*) 'Processor',MyID,' Reduce finished'
+ evdw=energia(1)
+ evdw2=energia(2)
+ ees=energia(3)
+ evdw1=energia(4)
+ ecorr=energia(5)
+ etors=energia(6)
+ ebe=energia(7)
+ escloc=energia(8)
+ ehpb=energia(9)
+ edihcnstr=energia(10)
+ eel_loc=energia(11)
+ ecorr5=energia(12)
+ ecorr6=energia(13)
+ eello_turn3=energia(14)
+ eello_turn4=energia(15)
+ eturn6=energia(16)
+ etors_d=energia(17)
+ endif
+c if (MyID.eq.BossID) then
+#endif
+ etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
+ & +wang*ebe+wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5
+ & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
+ & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
+ energia(0)=etot
+ energia(1)=evdw
+ energia(2)=evdw2
+ energia(3)=ees+evdw1
+ energia(4)=ecorr
+ energia(5)=ecorr5
+ energia(6)=ecorr6
+ energia(7)=eel_loc
+ energia(8)=eello_turn3
+ energia(9)=eello_turn4
+ energia(10)=eturn6
+ energia(11)=ebe
+ energia(12)=escloc
+ energia(13)=etors
+ energia(14)=etors_d
+ energia(15)=ehpb
+ energia(16)=edihcnstr
+ energia(17)=evdw2_14
+c detecting NaNQ
+ i=0
+#ifdef WINPGI
+ idumm=proc_proc(etot,i)
+#else
+ call proc_proc(etot,i)
+#endif
+ if(i.eq.1)energia(0)=1.0d+99
+#ifdef MPL
+c endif
+#endif
+ if (calc_grad) then
+C
+C Sum up the components of the Cartesian gradient.
+C
+ do i=1,nct
+ do j=1,3
+ gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
+ & welec*gelc(j,i)+wstrain*ghpbc(j,i)+
+ & wcorr*gradcorr(j,i)+
+ & wel_loc*gel_loc(j,i)/eel_loc_scal+
+ & wturn3*gcorr3_turn(j,i)/eello_turn3_scal+
+ & wturn4*gcorr4_turn(j,i)/eello_turn4_scal+
+ & wcorr5*gradcorr5(j,i)/ecorr5_scal+
+ & wcorr6*gradcorr6(j,i)/ecorr6_scal+
+ & wturn6*gcorr6_turn(j,i)/eturn6_scal
+ gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)
+ enddo
+cd print '(i3,9(1pe12.4))',i,(gvdwc(k,i),k=1,3),(gelc(k,i),k=1,3),
+cd & (gradc(k,i),k=1,3)
+ enddo
+
+
+ do i=1,nres-3
+cd write (iout,*) i,g_corr5_loc(i)
+ gloc(i,icg)=gloc(i,icg)+wcorr*gcorr_loc(i)
+ & +wcorr5*g_corr5_loc(i)/ecorr5_scal
+ & +wcorr6*g_corr6_loc(i)/ecorr6_scal
+ & +wturn4*gel_loc_turn4(i)/eello_turn4_scal
+ & +wturn3*gel_loc_turn3(i)/eello_turn3_scal
+ & +wturn6*gel_loc_turn6(i)/eturn6_scal
+ & +wel_loc*gel_loc_loc(i)/eel_loc_scal
+ enddo
+ endif
+cd print*,evdw,wsc,evdw2,wscp,ees+evdw1,welec,ebe,wang,
+cd & escloc,wscloc,etors,wtor,ehpb,wstrain,nss,ebr,etot
+cd call enerprint(energia(0))
+cd call intout
+cd stop
+ return
+ end
+C------------------------------------------------------------------------
+ subroutine enerprint(energia)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ double precision energia(0:max_ene)
+ etot=energia(0)
+ evdw=energia(1)
+ evdw2=energia(2)
+ ees=energia(3)
+ ecorr=energia(4)
+ ecorr5=energia(5)
+ ecorr6=energia(6)
+ eel_loc=energia(7)
+ eello_turn3=energia(8)
+ eello_turn4=energia(9)
+ eello_turn6=energia(10)
+ ebe=energia(11)
+ escloc=energia(12)
+ etors=energia(13)
+ etors_d=energia(14)
+ ehpb=energia(15)
+ edihcnstr=energia(16)
+ write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,ebe,wang,
+ & escloc,wscloc,etors,wtor,etors_d,wtor_d,ehpb,wstrain,
+ & ecorr,wcorr,
+ & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
+ & eello_turn4,wturn4,eello_turn6,wturn6,edihcnstr,ebr*nss,etot
+ 10 format (/'Virtual-chain energies:'//
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
+ & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
+ & ' (SS bridges & dist. cnstr.)'/
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
+ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
+ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
+ & 'ETOT= ',1pE16.6,' (total)')
+ return
+ end
+C-----------------------------------------------------------------------
+ subroutine elj(evdw)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the LJ potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ parameter (accur=1.0d-10)
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.TORSION'
+ include 'COMMON.ENEPS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CONTACTS'
+ dimension gg(3)
+ integer icant
+ external icant
+cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+C Change 12/1/95
+ num_conti=0
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
+cd & 'iend=',iend(i,iint)
+ do j=istart(i,iint),iend(i,iint)
+ itypj=itype(j)
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+C Change 12/1/95 to calculate four-body interactions
+ rij=xj*xj+yj*yj+zj*zj
+ rrij=1.0D0/rij
+c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
+ eps0ij=eps(itypi,itypj)
+ fac=rrij**expon2
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=e1+e2
+ ij=icant(itypi,itypj)
+ eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
+cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
+cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
+ evdw=evdw+evdwij
+ if (calc_grad) then
+C
+C Calculate the components of the gradient in DC and X
+C
+ fac=-rrij*(e1+evdwij)
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ enddo
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ endif
+C
+C 12/1/95, revised on 5/20/97
+C
+C Calculate the contact function. The ith column of the array JCONT will
+C contain the numbers of atoms that make contacts with the atom I (of numbers
+C greater than I). The arrays FACONT and GACONT will contain the values of
+C the contact function and its derivative.
+C
+C Uncomment next line, if the correlation interactions include EVDW explicitly.
+c if (j.gt.i+1 .and. evdwij.le.0.0D0) then
+C Uncomment next line, if the correlation interactions are contact function only
+ if (j.gt.i+1.and. eps0ij.gt.0.0D0) then
+ rij=dsqrt(rij)
+ sigij=sigma(itypi,itypj)
+ r0ij=rs0(itypi,itypj)
+C
+C Check whether the SC's are not too far to make a contact.
+C
+ rcut=1.5d0*r0ij
+ call gcont(rij,rcut,1.0d0,0.2d0*rcut,fcont,fprimcont)
+C Add a new contact, if the SC's are close enough, but not too close (r<sigma).
+C
+ if (fcont.gt.0.0D0) then
+C If the SC-SC distance if close to sigma, apply spline.
+cAdam call gcont(-rij,-1.03d0*sigij,2.0d0*sigij,1.0d0,
+cAdam & fcont1,fprimcont1)
+cAdam fcont1=1.0d0-fcont1
+cAdam if (fcont1.gt.0.0d0) then
+cAdam fprimcont=fprimcont*fcont1+fcont*fprimcont1
+cAdam fcont=fcont*fcont1
+cAdam endif
+C Uncomment following 4 lines to have the geometric average of the epsilon0's
+cga eps0ij=1.0d0/dsqrt(eps0ij)
+cga do k=1,3
+cga gg(k)=gg(k)*eps0ij
+cga enddo
+cga eps0ij=-evdwij*eps0ij
+C Uncomment for AL's type of SC correlation interactions.
+cadam eps0ij=-evdwij
+ num_conti=num_conti+1
+ jcont(num_conti,i)=j
+ facont(num_conti,i)=fcont*eps0ij
+ fprimcont=eps0ij*fprimcont/rij
+ fcont=expon*fcont
+cAdam gacont(1,num_conti,i)=-fprimcont*xj+fcont*gg(1)
+cAdam gacont(2,num_conti,i)=-fprimcont*yj+fcont*gg(2)
+cAdam gacont(3,num_conti,i)=-fprimcont*zj+fcont*gg(3)
+C Uncomment following 3 lines for Skolnick's type of SC correlation.
+ gacont(1,num_conti,i)=-fprimcont*xj
+ gacont(2,num_conti,i)=-fprimcont*yj
+ gacont(3,num_conti,i)=-fprimcont*zj
+cd write (iout,'(2i5,2f10.5)') i,j,rij,facont(num_conti,i)
+cd write (iout,'(2i3,3f10.5)')
+cd & i,j,(gacont(kk,num_conti,i),kk=1,3)
+ endif
+ endif
+ enddo ! j
+ enddo ! iint
+C Change 12/1/95
+ num_cont(i)=num_conti
+ enddo ! i
+ if (calc_grad) then
+ do i=1,nct
+ do j=1,3
+ gvdwc(j,i)=expon*gvdwc(j,i)
+ gvdwx(j,i)=expon*gvdwx(j,i)
+ enddo
+ enddo
+ endif
+C******************************************************************************
+C
+C N O T E !!!
+C
+C To save time, the factor of EXPON has been extracted from ALL components
+C of GVDWC and GRADX. Remember to multiply them by this factor before further
+C use!
+C
+C******************************************************************************
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine eljk(evdw)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the LJK potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ dimension gg(3)
+ logical scheck
+ integer icant
+ external icant
+c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ itypj=itype(j)
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ fac_augm=rrij**expon
+ e_augm=augm(itypi,itypj)*fac_augm
+ r_inv_ij=dsqrt(rrij)
+ rij=1.0D0/r_inv_ij
+ r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
+ fac=r_shift_inv**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=e_augm+e1+e2
+ ij=icant(itypi,itypj)
+ eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm)
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps(itypi,itypj)
+cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
+cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
+cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
+ evdw=evdw+evdwij
+ if (calc_grad) then
+C
+C Calculate the components of the gradient in DC and X
+C
+ fac=-2.0D0*rrij*e_augm-r_inv_ij*r_shift_inv*(e1+e1+e2)
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ enddo
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ if (calc_grad) then
+ do i=1,nct
+ do j=1,3
+ gvdwc(j,i)=expon*gvdwc(j,i)
+ gvdwx(j,i)=expon*gvdwx(j,i)
+ enddo
+ enddo
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine ebp(evdw)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Berne-Pechukas potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ common /srutu/ icall
+c double precision rrsave(maxdim)
+ logical lprn
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+c print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
+ evdw=0.0D0
+c if (icall.eq.0) then
+c lprn=.true.
+c else
+ lprn=.false.
+c endif
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=dsc_inv(itypi)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=dsc_inv(itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+cd if (icall.eq.0) then
+cd rrsave(ind)=rrij
+cd else
+cd rrij=rrsave(ind)
+cd endif
+ rij=dsqrt(rrij)
+C Calculate the angle-dependent terms of energy & contributions to derivatives.
+ call sc_angular
+C Calculate whole angle-dependent part of epsilon and contributions
+C to its derivatives
+ fac=(rrij*sigsq)**expon2
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ evdwij=evdwij*eps2rt*eps3rt
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj)
+ evdw=evdw+evdwij
+ if (calc_grad) then
+ if (lprn) then
+ sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
+cd & restyp(itypi),i,restyp(itypj),j,
+cd & epsi,sigm,chi1,chi2,chip1,chip2,
+cd & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
+cd & om1,om2,om12,1.0D0/dsqrt(rrij),
+cd & evdwij
+ endif
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)
+ sigder=fac/sigsq
+ fac=rrij*fac
+C Calculate radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate the angular part of the gradient and sum add the contributions
+C to the appropriate components of the Cartesian gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+c stop
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine egb(evdw)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Gay-Berne potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ logical lprn
+ common /srutu/icall
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+ evdw=0.0D0
+ lprn=.false.
+c if (icall.gt.0) lprn=.true.
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=dsc_inv(itypi)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=dsc_inv(itypj)
+ sig0ij=sigma(itypi,itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of energy and contributions to their
+C derivatives.
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+sig0ij
+C I hate to put IF's in the loops, but here don't have another choice!!!!
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
+ return
+ endif
+ sigder=-sig*sigsq
+c---------------------------------------------------------------
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ evdwij=evdwij*eps2rt*eps3rt
+ evdw=evdw+evdwij
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
+c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
+c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
+c & aux*e2/eps(itypi,itypj)
+c if (lprn) then
+c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+c epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+c & restyp(itypi),i,restyp(itypj),j,
+c & epsi,sigm,chi1,chi2,chip1,chip2,
+c & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
+c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+c & evdwij
+c endif
+ if (calc_grad) then
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac
+C Calculate the radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate angular part of the gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ end
+C-----------------------------------------------------------------------------
+ subroutine egbv(evdw)
+C
+C This subroutine calculates the interaction energy of nonbonded side chains
+C assuming the Gay-Berne-Vorobjev potential of interaction.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.ENEPS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ common /srutu/ icall
+ logical lprn
+ integer icant
+ external icant
+ do i=1,210
+ do j=1,2
+ eneps_temp(j,i)=0.0d0
+ enddo
+ enddo
+ evdw=0.0D0
+c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
+ evdw=0.0D0
+ lprn=.false.
+c if (icall.gt.0) lprn=.true.
+ ind=0
+ do i=iatsc_s,iatsc_e
+ itypi=itype(i)
+ itypi1=itype(i+1)
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=dsc_inv(itypi)
+C
+C Calculate SC interaction energy.
+C
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ ind=ind+1
+ itypj=itype(j)
+ dscj_inv=dsc_inv(itypj)
+ sig0ij=sigma(itypi,itypj)
+ r0ij=r0(itypi,itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
+C For diagnostics only!!!
+c chi1=0.0D0
+c chi2=0.0D0
+c chi12=0.0D0
+c chip1=0.0D0
+c chip2=0.0D0
+c chip12=0.0D0
+c alf1=0.0D0
+c alf2=0.0D0
+c alf12=0.0D0
+ xj=c(1,nres+j)-xi
+ yj=c(2,nres+j)-yi
+ zj=c(3,nres+j)-zi
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+C Calculate angle-dependent terms of energy and contributions to their
+C derivatives.
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+r0ij
+C I hate to put IF's in the loops, but here don't have another choice!!!!
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
+ return
+ endif
+ sigder=-sig*sigsq
+c---------------------------------------------------------------
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
+ e1=fac*fac*aa(itypi,itypj)
+ e2=fac*bb(itypi,itypj)
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ fac_augm=rrij**expon
+ e_augm=augm(itypi,itypj)*fac_augm
+ evdwij=evdwij*eps2rt*eps3rt
+ evdw=evdw+evdwij+e_augm
+ ij=icant(itypi,itypj)
+ aux=eps1*eps2rt**2*eps3rt**2
+ eneps_temp(1,ij)=eneps_temp(1,ij)+aux*(e1+e_augm)
+ & /dabs(eps(itypi,itypj))
+ eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
+c eneps_temp(ij)=eneps_temp(ij)
+c & +(evdwij+e_augm)/eps(itypi,itypj)
+c if (lprn) then
+c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+c epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+c & restyp(itypi),i,restyp(itypj),j,
+c & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
+c & chi1,chi2,chip1,chip2,
+c & eps1,eps2rt**2,eps3rt**2,
+c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+c & evdwij+e_augm
+c endif
+ if (calc_grad) then
+C Calculate gradient components.
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac-2*expon*rrij*e_augm
+C Calculate the radial part of the gradient
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
+C Calculate angular part of the gradient.
+ call sc_grad
+ endif
+ enddo ! j
+ enddo ! iint
+ enddo ! i
+ end
+C-----------------------------------------------------------------------------
+ subroutine sc_angular
+C Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
+C om12. Called by ebp, egb, and egbv.
+ implicit none
+ include 'COMMON.CALC'
+ erij(1)=xj*rij
+ erij(2)=yj*rij
+ erij(3)=zj*rij
+ om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
+ om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
+ om12=dxi*dxj+dyi*dyj+dzi*dzj
+ chiom12=chi12*om12
+C Calculate eps1(om12) and its derivative in om12
+ faceps1=1.0D0-om12*chiom12
+ faceps1_inv=1.0D0/faceps1
+ eps1=dsqrt(faceps1_inv)
+C Following variable is eps1*deps1/dom12
+ eps1_om12=faceps1_inv*chiom12
+C Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
+C and om12.
+ om1om2=om1*om2
+ chiom1=chi1*om1
+ chiom2=chi2*om2
+ facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
+ sigsq=1.0D0-facsig*faceps1_inv
+ sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
+ sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
+ sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
+C Calculate eps2 and its derivatives in om1, om2, and om12.
+ chipom1=chip1*om1
+ chipom2=chip2*om2
+ chipom12=chip12*om12
+ facp=1.0D0-om12*chipom12
+ facp_inv=1.0D0/facp
+ facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
+C Following variable is the square root of eps2
+ eps2rt=1.0D0-facp1*facp_inv
+C Following three variables are the derivatives of the square root of eps
+C in om1, om2, and om12.
+ eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
+ eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
+ eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
+C Evaluate the "asymmetric" factor in the VDW constant, eps3
+ eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
+C Calculate whole angle-dependent part of epsilon and contributions
+C to its derivatives
+ return
+ end
+C----------------------------------------------------------------------------
+ subroutine sc_grad
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.CALC'
+ double precision dcosom1(3),dcosom2(3)
+ eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
+ eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
+ eom12=evdwij*eps1_om12+eps2der*eps2rt_om12
+ & -2.0D0*alf12*eps3der+sigder*sigsq_om12
+ do k=1,3
+ dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
+ dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
+ enddo
+ do k=1,3
+ gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
+ enddo
+ do k=1,3
+ gvdwx(k,i)=gvdwx(k,i)-gg(k)
+ & +(eom12*dc_norm(k,nres+j)+eom1*erij(k))*dsci_inv
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)
+ & +(eom12*dc_norm(k,nres+i)+eom2*erij(k))*dscj_inv
+ enddo
+C
+C Calculate the components of the gradient in DC and X
+C
+ do k=i,j-1
+ do l=1,3
+ gvdwc(l,k)=gvdwc(l,k)+gg(l)
+ enddo
+ enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine vec_and_deriv
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ dimension uyder(3,3,2),uzder(3,3,2)
+C Compute the local reference systems. For reference system (i), the
+C X-axis points from CA(i) to CA(i+1), the Y axis is in the
+C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
+ do i=1,nres-1
+ if (i.eq.nres-1 .or. itel(i+1).eq.0) then
+C Case of the last full residue
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
+ costh=dcos(pi-theta(nres))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i-1)
+ uzder(3,1,1)= dc_norm(2,i-1)
+ uzder(1,2,1)= dc_norm(3,i-1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i-1)
+ uzder(1,3,1)=-dc_norm(2,i-1)
+ uzder(2,3,1)= dc_norm(1,i-1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+ endif
+C Compute the Y-axis
+ facy=fac
+ do k=1,3
+ uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i-1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+ uyder(j,j,1)=uyder(j,j,1)-costh
+ uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ else
+C Other residues
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
+ costh=dcos(pi-theta(i+2))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i+1)
+ uzder(3,1,1)= dc_norm(2,i+1)
+ uzder(1,2,1)= dc_norm(3,i+1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i+1)
+ uzder(1,3,1)=-dc_norm(2,i+1)
+ uzder(2,3,1)= dc_norm(1,i+1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+ endif
+C Compute the Y-axis
+ facy=fac
+ do k=1,3
+ uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ enddo
+ if (calc_grad) then
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i+1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+ uyder(j,j,1)=uyder(j,j,1)-costh
+ uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ endif
+ enddo
+ if (calc_grad) then
+ do i=1,nres-1
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i)
+ uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine vec_and_deriv_test
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ dimension uyder(3,3,2),uzder(3,3,2)
+C Compute the local reference systems. For reference system (i), the
+C X-axis points from CA(i) to CA(i+1), the Y axis is in the
+C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
+ do i=1,nres-1
+ if (i.eq.nres-1) then
+C Case of the last full residue
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
+ costh=dcos(pi-theta(nres))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+c write (iout,*) 'fac',fac,
+c & 1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i-1)
+ uzder(3,1,1)= dc_norm(2,i-1)
+ uzder(1,2,1)= dc_norm(3,i-1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i-1)
+ uzder(1,3,1)=-dc_norm(2,i-1)
+ uzder(2,3,1)= dc_norm(1,i-1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+C Compute the Y-axis
+ do k=1,3
+ uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
+ enddo
+ facy=fac
+ facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
+ & (scalar(dc_norm(1,i-1),dc_norm(1,i-1))**2-
+ & scalar(dc_norm(1,i),dc_norm(1,i-1))**2))
+ do k=1,3
+c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ uy(k,i)=
+c & facy*(
+ & dc_norm(k,i-1)*scalar(dc_norm(1,i),dc_norm(1,i))
+ & -scalar(dc_norm(1,i),dc_norm(1,i-1))*dc_norm(k,i)
+c & )
+ enddo
+c write (iout,*) 'facy',facy,
+c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ do k=1,3
+ uy(k,i)=facy*uy(k,i)
+ enddo
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i-1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+c uyder(j,j,1)=uyder(j,j,1)-costh
+c uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ uyder(j,j,1)=uyder(j,j,1)
+ & -scalar(dc_norm(1,i),dc_norm(1,i-1))
+ uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
+ & +uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ else
+C Other residues
+C Compute the Z-axis
+ call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
+ costh=dcos(pi-theta(i+2))
+ fac=1.0d0/dsqrt(1.0d0-costh*costh)
+ fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
+ do k=1,3
+ uz(k,i)=fac*uz(k,i)
+ enddo
+C Compute the derivatives of uz
+ uzder(1,1,1)= 0.0d0
+ uzder(2,1,1)=-dc_norm(3,i+1)
+ uzder(3,1,1)= dc_norm(2,i+1)
+ uzder(1,2,1)= dc_norm(3,i+1)
+ uzder(2,2,1)= 0.0d0
+ uzder(3,2,1)=-dc_norm(1,i+1)
+ uzder(1,3,1)=-dc_norm(2,i+1)
+ uzder(2,3,1)= dc_norm(1,i+1)
+ uzder(3,3,1)= 0.0d0
+ uzder(1,1,2)= 0.0d0
+ uzder(2,1,2)= dc_norm(3,i)
+ uzder(3,1,2)=-dc_norm(2,i)
+ uzder(1,2,2)=-dc_norm(3,i)
+ uzder(2,2,2)= 0.0d0
+ uzder(3,2,2)= dc_norm(1,i)
+ uzder(1,3,2)= dc_norm(2,i)
+ uzder(2,3,2)=-dc_norm(1,i)
+ uzder(3,3,2)= 0.0d0
+C Compute the Y-axis
+ facy=fac
+ facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
+ & (scalar(dc_norm(1,i+1),dc_norm(1,i+1))**2-
+ & scalar(dc_norm(1,i),dc_norm(1,i+1))**2))
+ do k=1,3
+c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
+ uy(k,i)=
+c & facy*(
+ & dc_norm(k,i+1)*scalar(dc_norm(1,i),dc_norm(1,i))
+ & -scalar(dc_norm(1,i),dc_norm(1,i+1))*dc_norm(k,i)
+c & )
+ enddo
+c write (iout,*) 'facy',facy,
+c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
+ do k=1,3
+ uy(k,i)=facy*uy(k,i)
+ enddo
+C Compute the derivatives of uy
+ do j=1,3
+ do k=1,3
+ uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
+ & -dc_norm(k,i)*dc_norm(j,i+1)
+ uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
+ enddo
+c uyder(j,j,1)=uyder(j,j,1)-costh
+c uyder(j,j,2)=1.0d0+uyder(j,j,2)
+ uyder(j,j,1)=uyder(j,j,1)
+ & -scalar(dc_norm(1,i),dc_norm(1,i+1))
+ uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
+ & +uyder(j,j,2)
+ enddo
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=uyder(l,k,j)
+ uzgrad(l,k,j,i)=uzder(l,k,j)
+ enddo
+ enddo
+ enddo
+ call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
+ call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
+ call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
+ call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
+ endif
+ enddo
+ do i=1,nres-1
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i)
+ uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine check_vecgrad
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VECTORS'
+ dimension uygradt(3,3,2,maxres),uzgradt(3,3,2,maxres)
+ dimension uyt(3,maxres),uzt(3,maxres)
+ dimension uygradn(3,3,2),uzgradn(3,3,2),erij(3)
+ double precision delta /1.0d-7/
+ call vec_and_deriv
+cd do i=1,nres
+crc write(iout,'(2i5,2(3f10.5,5x))') i,1,dc_norm(:,i)
+crc write(iout,'(2i5,2(3f10.5,5x))') i,2,uy(:,i)
+crc write(iout,'(2i5,2(3f10.5,5x)/)')i,3,uz(:,i)
+cd write(iout,'(2i5,2(3f10.5,5x))') i,1,
+cd & (dc_norm(if90,i),if90=1,3)
+cd write(iout,'(2i5,2(3f10.5,5x))') i,2,(uy(if90,i),if90=1,3)
+cd write(iout,'(2i5,2(3f10.5,5x)/)')i,3,(uz(if90,i),if90=1,3)
+cd write(iout,'(a)')
+cd enddo
+ do i=1,nres
+ do j=1,2
+ do k=1,3
+ do l=1,3
+ uygradt(l,k,j,i)=uygrad(l,k,j,i)
+ uzgradt(l,k,j,i)=uzgrad(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ call vec_and_deriv_test
+ do i=1,nres
+ do j=1,3
+ uyt(j,i)=uy(j,i)
+ uzt(j,i)=uz(j,i)
+ enddo
+ enddo
+ do i=1,nres
+cd write (iout,*) 'i=',i
+ do k=1,3
+ erij(k)=dc_norm(k,i)
+ enddo
+ do j=1,3
+ do k=1,3
+ dc_norm(k,i)=erij(k)
+ enddo
+ dc_norm(j,i)=dc_norm(j,i)+delta
+c fac=dsqrt(scalar(dc_norm(1,i),dc_norm(1,i)))
+c do k=1,3
+c dc_norm(k,i)=dc_norm(k,i)/fac
+c enddo
+c write (iout,*) (dc_norm(k,i),k=1,3)
+c write (iout,*) (erij(k),k=1,3)
+ call vec_and_deriv_test
+ do k=1,3
+ uygradn(k,j,1)=(uy(k,i)-uyt(k,i))/delta
+ uygradn(k,j,2)=(uy(k,i-1)-uyt(k,i-1))/delta
+ uzgradn(k,j,1)=(uz(k,i)-uzt(k,i))/delta
+ uzgradn(k,j,2)=(uz(k,i-1)-uzt(k,i-1))/delta
+ enddo
+c write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+c & j,(uzgradt(k,j,1,i),k=1,3),(uzgradn(k,j,1),k=1,3),
+c & (uzgradt(k,j,2,i-1),k=1,3),(uzgradn(k,j,2),k=1,3)
+ enddo
+ do k=1,3
+ dc_norm(k,i)=erij(k)
+ enddo
+cd do k=1,3
+cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+cd & k,(uygradt(k,l,1,i),l=1,3),(uygradn(k,l,1),l=1,3),
+cd & (uygradt(k,l,2,i-1),l=1,3),(uygradn(k,l,2),l=1,3)
+cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
+cd & k,(uzgradt(k,l,1,i),l=1,3),(uzgradn(k,l,1),l=1,3),
+cd & (uzgradt(k,l,2,i-1),l=1,3),(uzgradn(k,l,2),l=1,3)
+cd write (iout,'(a)')
+cd enddo
+ enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine set_matrices
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ double precision auxvec(2),auxmat(2,2)
+C
+C Compute the virtual-bond-torsional-angle dependent quantities needed
+C to calculate the el-loc multibody terms of various order.
+C
+ do i=3,nres+1
+ if (i .lt. nres+1) then
+ sin1=dsin(phi(i))
+ cos1=dcos(phi(i))
+ sintab(i-2)=sin1
+ costab(i-2)=cos1
+ obrot(1,i-2)=cos1
+ obrot(2,i-2)=sin1
+ sin2=dsin(2*phi(i))
+ cos2=dcos(2*phi(i))
+ sintab2(i-2)=sin2
+ costab2(i-2)=cos2
+ obrot2(1,i-2)=cos2
+ obrot2(2,i-2)=sin2
+ Ug(1,1,i-2)=-cos1
+ Ug(1,2,i-2)=-sin1
+ Ug(2,1,i-2)=-sin1
+ Ug(2,2,i-2)= cos1
+ Ug2(1,1,i-2)=-cos2
+ Ug2(1,2,i-2)=-sin2
+ Ug2(2,1,i-2)=-sin2
+ Ug2(2,2,i-2)= cos2
+ else
+ costab(i-2)=1.0d0
+ sintab(i-2)=0.0d0
+ obrot(1,i-2)=1.0d0
+ obrot(2,i-2)=0.0d0
+ obrot2(1,i-2)=0.0d0
+ obrot2(2,i-2)=0.0d0
+ Ug(1,1,i-2)=1.0d0
+ Ug(1,2,i-2)=0.0d0
+ Ug(2,1,i-2)=0.0d0
+ Ug(2,2,i-2)=1.0d0
+ Ug2(1,1,i-2)=0.0d0
+ Ug2(1,2,i-2)=0.0d0
+ Ug2(2,1,i-2)=0.0d0
+ Ug2(2,2,i-2)=0.0d0
+ endif
+ if (i .gt. 3 .and. i .lt. nres+1) then
+ obrot_der(1,i-2)=-sin1
+ obrot_der(2,i-2)= cos1
+ Ugder(1,1,i-2)= sin1
+ Ugder(1,2,i-2)=-cos1
+ Ugder(2,1,i-2)=-cos1
+ Ugder(2,2,i-2)=-sin1
+ dwacos2=cos2+cos2
+ dwasin2=sin2+sin2
+ obrot2_der(1,i-2)=-dwasin2
+ obrot2_der(2,i-2)= dwacos2
+ Ug2der(1,1,i-2)= dwasin2
+ Ug2der(1,2,i-2)=-dwacos2
+ Ug2der(2,1,i-2)=-dwacos2
+ Ug2der(2,2,i-2)=-dwasin2
+ else
+ obrot_der(1,i-2)=0.0d0
+ obrot_der(2,i-2)=0.0d0
+ Ugder(1,1,i-2)=0.0d0
+ Ugder(1,2,i-2)=0.0d0
+ Ugder(2,1,i-2)=0.0d0
+ Ugder(2,2,i-2)=0.0d0
+ obrot2_der(1,i-2)=0.0d0
+ obrot2_der(2,i-2)=0.0d0
+ Ug2der(1,1,i-2)=0.0d0
+ Ug2der(1,2,i-2)=0.0d0
+ Ug2der(2,1,i-2)=0.0d0
+ Ug2der(2,2,i-2)=0.0d0
+ endif
+ if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
+ iti = itortyp(itype(i-2))
+ else
+ iti=ntortyp+1
+ endif
+ if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+cd write (iout,*) '*******i',i,' iti1',iti
+cd write (iout,*) 'b1',b1(:,iti)
+cd write (iout,*) 'b2',b2(:,iti)
+cd write (iout,*) 'Ug',Ug(:,:,i-2)
+ if (i .gt. iatel_s+2) then
+ call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2))
+ call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2))
+ call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2))
+ call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2))
+ call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2))
+ call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2))
+ call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2))
+ else
+ do k=1,2
+ Ub2(k,i-2)=0.0d0
+ Ctobr(k,i-2)=0.0d0
+ Dtobr2(k,i-2)=0.0d0
+ do l=1,2
+ EUg(l,k,i-2)=0.0d0
+ CUg(l,k,i-2)=0.0d0
+ DUg(l,k,i-2)=0.0d0
+ DtUg2(l,k,i-2)=0.0d0
+ enddo
+ enddo
+ endif
+ call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2))
+ call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2))
+ call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2))
+ call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2))
+ call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
+ call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2))
+ call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2))
+ do k=1,2
+ muder(k,i-2)=Ub2der(k,i-2)
+ enddo
+ if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+ do k=1,2
+ mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
+ enddo
+C Vectors and matrices dependent on a single virtual-bond dihedral.
+ call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
+ call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
+ call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2))
+ call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2))
+ call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2))
+ call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2))
+ call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2))
+cd write (iout,*) 'i',i,' mu ',(mu(k,i-2),k=1,2),
+cd & ' mu1',(b1(k,i-2),k=1,2),' mu2',(Ub2(k,i-2),k=1,2)
+ enddo
+C Matrices dependent on two consecutive virtual-bond dihedrals.
+C The order of matrices is from left to right.
+ do i=2,nres-1
+ call matmat2(DtUg2(1,1,i-1),EUg(1,1,i),DtUg2EUg(1,1,i))
+ call matmat2(DtUg2der(1,1,i-1),EUg(1,1,i),DtUg2EUgder(1,1,1,i))
+ call matmat2(DtUg2(1,1,i-1),EUgder(1,1,i),DtUg2EUgder(1,1,2,i))
+ call transpose2(DtUg2(1,1,i-1),auxmat(1,1))
+ call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUg(1,1,i))
+ call matmat2(auxmat(1,1),EUgder(1,1,i),Ug2DtEUgder(1,1,2,i))
+ call transpose2(DtUg2der(1,1,i-1),auxmat(1,1))
+ call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i))
+ enddo
+cd do i=1,nres
+cd iti = itortyp(itype(i))
+cd write (iout,*) i
+cd do j=1,2
+cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
+cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
+cd enddo
+cd enddo
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
+C
+C This subroutine calculates the average interaction energy and its gradient
+C in the virtual-bond vectors between non-adjacent peptide groups, based on
+C the potential described in Liwo et al., Protein Sci., 1993, 2, 1715.
+C The potential depends both on the distance of peptide-group centers and on
+C the orientation of the CA-CA virtual bonds.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
+ & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
+ double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1
+c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
+ double precision scal_el /0.5d0/
+C 12/13/98
+C 13-go grudnia roku pamietnego...
+ double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
+ & 0.0d0,1.0d0,0.0d0,
+ & 0.0d0,0.0d0,1.0d0/
+cd write(iout,*) 'In EELEC'
+cd do i=1,nloctyp
+cd write(iout,*) 'Type',i
+cd write(iout,*) 'B1',B1(:,i)
+cd write(iout,*) 'B2',B2(:,i)
+cd write(iout,*) 'CC',CC(:,:,i)
+cd write(iout,*) 'DD',DD(:,:,i)
+cd write(iout,*) 'EE',EE(:,:,i)
+cd enddo
+cd call check_vecgrad
+cd stop
+ if (icheckgrad.eq.1) then
+ do i=1,nres-1
+ fac=1.0d0/dsqrt(scalar(dc(1,i),dc(1,i)))
+ do k=1,3
+ dc_norm(k,i)=dc(k,i)*fac
+ enddo
+c write (iout,*) 'i',i,' fac',fac
+ enddo
+ endif
+ if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
+ & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or.
+ & wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then
+cd if (wel_loc.gt.0.0d0) then
+ if (icheckgrad.eq.1) then
+ call vec_and_deriv_test
+ else
+ call vec_and_deriv
+ endif
+ call set_matrices
+ endif
+cd do i=1,nres-1
+cd write (iout,*) 'i=',i
+cd do k=1,3
+cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i)
+cd enddo
+cd do k=1,3
+cd write (iout,'(f10.5,2x,3f10.5,2x,3f10.5)')
+cd & uz(k,i),(uzgrad(k,l,1,i),l=1,3),(uzgrad(k,l,2,i),l=1,3)
+cd enddo
+cd enddo
+ num_conti_hb=0
+ ees=0.0D0
+ evdw1=0.0D0
+ eel_loc=0.0d0
+ eello_turn3=0.0d0
+ eello_turn4=0.0d0
+ ind=0
+ do i=1,nres
+ num_cont_hb(i)=0
+ enddo
+cd print '(a)','Enter EELEC'
+cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
+ do i=1,nres
+ gel_loc_loc(i)=0.0d0
+ gcorr_loc(i)=0.0d0
+ enddo
+ do i=iatel_s,iatel_e
+ if (itel(i).eq.0) goto 1215
+ dxi=dc(1,i)
+ dyi=dc(2,i)
+ dzi=dc(3,i)
+ dx_normi=dc_norm(1,i)
+ dy_normi=dc_norm(2,i)
+ dz_normi=dc_norm(3,i)
+ xmedi=c(1,i)+0.5d0*dxi
+ ymedi=c(2,i)+0.5d0*dyi
+ zmedi=c(3,i)+0.5d0*dzi
+ num_conti=0
+c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
+ do j=ielstart(i),ielend(i)
+ if (itel(j).eq.0) goto 1216
+ ind=ind+1
+ iteli=itel(i)
+ itelj=itel(j)
+ if (j.eq.i+2 .and. itelj.eq.2) iteli=2
+ aaa=app(iteli,itelj)
+ bbb=bpp(iteli,itelj)
+C Diagnostics only!!!
+c aaa=0.0D0
+c bbb=0.0D0
+c ael6i=0.0D0
+c ael3i=0.0D0
+C End diagnostics
+ ael6i=ael6(iteli,itelj)
+ ael3i=ael3(iteli,itelj)
+ dxj=dc(1,j)
+ dyj=dc(2,j)
+ dzj=dc(3,j)
+ dx_normj=dc_norm(1,j)
+ dy_normj=dc_norm(2,j)
+ dz_normj=dc_norm(3,j)
+ xj=c(1,j)+0.5D0*dxj-xmedi
+ yj=c(2,j)+0.5D0*dyj-ymedi
+ zj=c(3,j)+0.5D0*dzj-zmedi
+ rij=xj*xj+yj*yj+zj*zj
+ rrmij=1.0D0/rij
+ rij=dsqrt(rij)
+ rmij=1.0D0/rij
+ r3ij=rrmij*rmij
+ r6ij=r3ij*r3ij
+ cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj
+ cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij
+ cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij
+ fac=cosa-3.0D0*cosb*cosg
+ ev1=aaa*r6ij*r6ij
+c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions
+ if (j.eq.i+2) ev1=scal_el*ev1
+ ev2=bbb*r6ij
+ fac3=ael6i*r6ij
+ fac4=ael3i*r3ij
+ evdwij=ev1+ev2
+ el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
+ el2=fac4*fac
+ eesij=el1+el2
+c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij
+C 12/26/95 - for the evaluation of multi-body H-bonding interactions
+ ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
+ ees=ees+eesij
+ evdw1=evdw1+evdwij
+cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
+cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
+cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
+cd & xmedi,ymedi,zmedi,xj,yj,zj
+C
+C Calculate contributions to the Cartesian gradient.
+C
+ facvdw=ev1+evdwij
+ facel=el1+eesij
+ fac1=fac
+ fac=-3*rrmij*(facvdw+facvdw+facel)
+ erij(1)=xj*rmij
+ erij(2)=yj*rmij
+ erij(3)=zj*rmij
+ if (calc_grad) then
+*
+* Radial derivatives. First process both termini of the fragment (i,j)
+*
+ ggg(1)=fac*xj
+ ggg(2)=fac*yj
+ ggg(3)=fac*zj
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gelc(k,i)=gelc(k,i)+ghalf
+ gelc(k,j)=gelc(k,j)+ghalf
+ enddo
+*
+* Loop over residues i+1 thru j-1.
+*
+ do k=i+1,j-1
+ do l=1,3
+ gelc(l,k)=gelc(l,k)+ggg(l)
+ enddo
+ enddo
+*
+* Angular part
+*
+ ecosa=2.0D0*fac3*fac1+fac4
+ fac4=-3.0D0*fac4
+ fac3=-6.0D0*fac3
+ ecosb=(fac3*(fac1*cosg+cosb)+cosg*fac4)
+ ecosg=(fac3*(fac1*cosb+cosg)+cosb*fac4)
+ do k=1,3
+ dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
+ dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
+ enddo
+cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
+cd & (dcosg(k),k=1,3)
+ do k=1,3
+ ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+ enddo
+ do k=1,3
+ ghalf=0.5D0*ggg(k)
+ gelc(k,i)=gelc(k,i)+ghalf
+ & +(ecosa*dc_norm(k,j)+ecosb*erij(k))*vblinv
+ gelc(k,j)=gelc(k,j)+ghalf
+ & +(ecosa*dc_norm(k,i)+ecosg*erij(k))*vblinv
+ enddo
+ do k=i+1,j-1
+ do l=1,3
+ gelc(l,k)=gelc(l,k)+ggg(l)
+ enddo
+ enddo
+ endif
+
+ IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
+ & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0
+ & .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
+C
+C 9/25/99 Mixed third-order local-electrostatic terms. The local-interaction
+C energy of a peptide unit is assumed in the form of a second-order
+C Fourier series in the angles lambda1 and lambda2 (see Nishikawa et al.
+C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms
+C are computed for EVERY pair of non-contiguous peptide groups.
+C
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ kkk=0
+ do k=1,2
+ do l=1,2
+ kkk=kkk+1
+ muij(kkk)=mu(k,i)*mu(l,j)
+ enddo
+ enddo
+cd write (iout,*) 'EELEC: i',i,' j',j
+cd write (iout,*) 'j',j,' j1',j1,' j2',j2
+cd write(iout,*) 'muij',muij
+ ury=scalar(uy(1,i),erij)
+ urz=scalar(uz(1,i),erij)
+ vry=scalar(uy(1,j),erij)
+ vrz=scalar(uz(1,j),erij)
+ a22=scalar(uy(1,i),uy(1,j))-3*ury*vry
+ a23=scalar(uy(1,i),uz(1,j))-3*ury*vrz
+ a32=scalar(uz(1,i),uy(1,j))-3*urz*vry
+ a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz
+C For diagnostics only
+cd a22=1.0d0
+cd a23=1.0d0
+cd a32=1.0d0
+cd a33=1.0d0
+ fac=dsqrt(-ael6i)*r3ij
+cd write (2,*) 'fac=',fac
+C For diagnostics only
+cd fac=1.0d0
+ a22=a22*fac
+ a23=a23*fac
+ a32=a32*fac
+ a33=a33*fac
+cd write (iout,'(4i5,4f10.5)')
+cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
+cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
+cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') (uy(k,i),k=1,3),
+cd & (uz(k,i),k=1,3),(uy(k,j),k=1,3),(uz(k,j),k=1,3)
+cd write (iout,'(4f10.5)')
+cd & scalar(uy(1,i),uy(1,j)),scalar(uy(1,i),uz(1,j)),
+cd & scalar(uz(1,i),uy(1,j)),scalar(uz(1,i),uz(1,j))
+cd write (iout,'(4f10.5)') ury,urz,vry,vrz
+cd write (iout,'(2i3,9f10.5/)') i,j,
+cd & fac22,a22,fac23,a23,fac32,a32,fac33,a33,eel_loc_ij
+ if (calc_grad) then
+C Derivatives of the elements of A in virtual-bond vectors
+ call unormderiv(erij(1),unmat(1,1),rmij,erder(1,1))
+cd do k=1,3
+cd do l=1,3
+cd erder(k,l)=0.0d0
+cd enddo
+cd enddo
+ do k=1,3
+ uryg(k,1)=scalar(erder(1,k),uy(1,i))
+ uryg(k,2)=scalar(uygrad(1,k,1,i),erij(1))
+ uryg(k,3)=scalar(uygrad(1,k,2,i),erij(1))
+ urzg(k,1)=scalar(erder(1,k),uz(1,i))
+ urzg(k,2)=scalar(uzgrad(1,k,1,i),erij(1))
+ urzg(k,3)=scalar(uzgrad(1,k,2,i),erij(1))
+ vryg(k,1)=scalar(erder(1,k),uy(1,j))
+ vryg(k,2)=scalar(uygrad(1,k,1,j),erij(1))
+ vryg(k,3)=scalar(uygrad(1,k,2,j),erij(1))
+ vrzg(k,1)=scalar(erder(1,k),uz(1,j))
+ vrzg(k,2)=scalar(uzgrad(1,k,1,j),erij(1))
+ vrzg(k,3)=scalar(uzgrad(1,k,2,j),erij(1))
+ enddo
+cd do k=1,3
+cd do l=1,3
+cd uryg(k,l)=0.0d0
+cd urzg(k,l)=0.0d0
+cd vryg(k,l)=0.0d0
+cd vrzg(k,l)=0.0d0
+cd enddo
+cd enddo
+C Compute radial contributions to the gradient
+ facr=-3.0d0*rrmij
+ a22der=a22*facr
+ a23der=a23*facr
+ a32der=a32*facr
+ a33der=a33*facr
+cd a22der=0.0d0
+cd a23der=0.0d0
+cd a32der=0.0d0
+cd a33der=0.0d0
+ agg(1,1)=a22der*xj
+ agg(2,1)=a22der*yj
+ agg(3,1)=a22der*zj
+ agg(1,2)=a23der*xj
+ agg(2,2)=a23der*yj
+ agg(3,2)=a23der*zj
+ agg(1,3)=a32der*xj
+ agg(2,3)=a32der*yj
+ agg(3,3)=a32der*zj
+ agg(1,4)=a33der*xj
+ agg(2,4)=a33der*yj
+ agg(3,4)=a33der*zj
+C Add the contributions coming from er
+ fac3=-3.0d0*fac
+ do k=1,3
+ agg(k,1)=agg(k,1)+fac3*(uryg(k,1)*vry+vryg(k,1)*ury)
+ agg(k,2)=agg(k,2)+fac3*(uryg(k,1)*vrz+vrzg(k,1)*ury)
+ agg(k,3)=agg(k,3)+fac3*(urzg(k,1)*vry+vryg(k,1)*urz)
+ agg(k,4)=agg(k,4)+fac3*(urzg(k,1)*vrz+vrzg(k,1)*urz)
+ enddo
+ do k=1,3
+C Derivatives in DC(i)
+ ghalf1=0.5d0*agg(k,1)
+ ghalf2=0.5d0*agg(k,2)
+ ghalf3=0.5d0*agg(k,3)
+ ghalf4=0.5d0*agg(k,4)
+ aggi(k,1)=fac*(scalar(uygrad(1,k,1,i),uy(1,j))
+ & -3.0d0*uryg(k,2)*vry)+ghalf1
+ aggi(k,2)=fac*(scalar(uygrad(1,k,1,i),uz(1,j))
+ & -3.0d0*uryg(k,2)*vrz)+ghalf2
+ aggi(k,3)=fac*(scalar(uzgrad(1,k,1,i),uy(1,j))
+ & -3.0d0*urzg(k,2)*vry)+ghalf3
+ aggi(k,4)=fac*(scalar(uzgrad(1,k,1,i),uz(1,j))
+ & -3.0d0*urzg(k,2)*vrz)+ghalf4
+C Derivatives in DC(i+1)
+ aggi1(k,1)=fac*(scalar(uygrad(1,k,2,i),uy(1,j))
+ & -3.0d0*uryg(k,3)*vry)+agg(k,1)
+ aggi1(k,2)=fac*(scalar(uygrad(1,k,2,i),uz(1,j))
+ & -3.0d0*uryg(k,3)*vrz)+agg(k,2)
+ aggi1(k,3)=fac*(scalar(uzgrad(1,k,2,i),uy(1,j))
+ & -3.0d0*urzg(k,3)*vry)+agg(k,3)
+ aggi1(k,4)=fac*(scalar(uzgrad(1,k,2,i),uz(1,j))
+ & -3.0d0*urzg(k,3)*vrz)+agg(k,4)
+C Derivatives in DC(j)
+ aggj(k,1)=fac*(scalar(uygrad(1,k,1,j),uy(1,i))
+ & -3.0d0*vryg(k,2)*ury)+ghalf1
+ aggj(k,2)=fac*(scalar(uzgrad(1,k,1,j),uy(1,i))
+ & -3.0d0*vrzg(k,2)*ury)+ghalf2
+ aggj(k,3)=fac*(scalar(uygrad(1,k,1,j),uz(1,i))
+ & -3.0d0*vryg(k,2)*urz)+ghalf3
+ aggj(k,4)=fac*(scalar(uzgrad(1,k,1,j),uz(1,i))
+ & -3.0d0*vrzg(k,2)*urz)+ghalf4
+C Derivatives in DC(j+1) or DC(nres-1)
+ aggj1(k,1)=fac*(scalar(uygrad(1,k,2,j),uy(1,i))
+ & -3.0d0*vryg(k,3)*ury)
+ aggj1(k,2)=fac*(scalar(uzgrad(1,k,2,j),uy(1,i))
+ & -3.0d0*vrzg(k,3)*ury)
+ aggj1(k,3)=fac*(scalar(uygrad(1,k,2,j),uz(1,i))
+ & -3.0d0*vryg(k,3)*urz)
+ aggj1(k,4)=fac*(scalar(uzgrad(1,k,2,j),uz(1,i))
+ & -3.0d0*vrzg(k,3)*urz)
+cd aggi(k,1)=ghalf1
+cd aggi(k,2)=ghalf2
+cd aggi(k,3)=ghalf3
+cd aggi(k,4)=ghalf4
+C Derivatives in DC(i+1)
+cd aggi1(k,1)=agg(k,1)
+cd aggi1(k,2)=agg(k,2)
+cd aggi1(k,3)=agg(k,3)
+cd aggi1(k,4)=agg(k,4)
+C Derivatives in DC(j)
+cd aggj(k,1)=ghalf1
+cd aggj(k,2)=ghalf2
+cd aggj(k,3)=ghalf3
+cd aggj(k,4)=ghalf4
+C Derivatives in DC(j+1)
+cd aggj1(k,1)=0.0d0
+cd aggj1(k,2)=0.0d0
+cd aggj1(k,3)=0.0d0
+cd aggj1(k,4)=0.0d0
+ if (j.eq.nres-1 .and. i.lt.j-2) then
+ do l=1,4
+ aggj1(k,l)=aggj1(k,l)+agg(k,l)
+cd aggj1(k,l)=agg(k,l)
+ enddo
+ endif
+ enddo
+ endif
+c goto 11111
+C Check the loc-el terms by numerical integration
+ acipa(1,1)=a22
+ acipa(1,2)=a23
+ acipa(2,1)=a32
+ acipa(2,2)=a33
+ a22=-a22
+ a23=-a23
+ do l=1,2
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ if (j.lt.nres-1) then
+ a22=-a22
+ a32=-a32
+ do l=1,3,2
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ else
+ a22=-a22
+ a23=-a23
+ a32=-a32
+ a33=-a33
+ do l=1,4
+ do k=1,3
+ agg(k,l)=-agg(k,l)
+ aggi(k,l)=-aggi(k,l)
+ aggi1(k,l)=-aggi1(k,l)
+ aggj(k,l)=-aggj(k,l)
+ aggj1(k,l)=-aggj1(k,l)
+ enddo
+ enddo
+ endif
+ ENDIF ! WCORR
+11111 continue
+ IF (wel_loc.gt.0.0d0) THEN
+C Contribution to the local-electrostatic energy coming from the i-j pair
+ eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
+ & +a33*muij(4)
+cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
+cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
+ eel_loc=eel_loc+eel_loc_ij
+C Partial derivatives in virtual-bond dihedral angles gamma
+ if (calc_grad) then
+ if (i.gt.1)
+ & gel_loc_loc(i-1)=gel_loc_loc(i-1)+
+ & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
+ & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)
+ gel_loc_loc(j-1)=gel_loc_loc(j-1)+
+ & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
+ & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)
+cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij)
+cd write(iout,*) 'agg ',agg
+cd write(iout,*) 'aggi ',aggi
+cd write(iout,*) 'aggi1',aggi1
+cd write(iout,*) 'aggj ',aggj
+cd write(iout,*) 'aggj1',aggj1
+
+C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
+ do l=1,3
+ ggg(l)=agg(l,1)*muij(1)+
+ & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)
+ enddo
+ do k=i+2,j2
+ do l=1,3
+ gel_loc(l,k)=gel_loc(l,k)+ggg(l)
+ enddo
+ enddo
+C Remaining derivatives of eello
+ do l=1,3
+ gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
+ gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
+ gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
+ gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
+ enddo
+ endif
+ ENDIF
+ if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
+C Contributions from turns
+ a_temp(1,1)=a22
+ a_temp(1,2)=a23
+ a_temp(2,1)=a32
+ a_temp(2,2)=a33
+ call eturn34(i,j,eello_turn3,eello_turn4)
+ endif
+C Change 12/26/95 to calculate four-body contributions to H-bonding energy
+ if (j.gt.i+1 .and. num_conti.le.maxconts) then
+C
+C Calculate the contact function. The ith column of the array JCONT will
+C contain the numbers of atoms that make contacts with the atom I (of numbers
+C greater than I). The arrays FACONT and GACONT will contain the values of
+C the contact function and its derivative.
+c r0ij=1.02D0*rpp(iteli,itelj)
+c r0ij=1.11D0*rpp(iteli,itelj)
+ r0ij=2.20D0*rpp(iteli,itelj)
+c r0ij=1.55D0*rpp(iteli,itelj)
+ call gcont(rij,r0ij,1.0D0,0.2d0*r0ij,fcont,fprimcont)
+ if (fcont.gt.0.0D0) then
+ num_conti=num_conti+1
+ if (num_conti.gt.maxconts) then
+ write (iout,*) 'WARNING - max. # of contacts exceeded;',
+ & ' will skip next contacts for this conf.'
+ else
+ jcont_hb(num_conti,i)=j
+ IF (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.
+ & wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
+C 9/30/99 (AL) - store components necessary to evaluate higher-order loc-el
+C terms.
+ d_cont(num_conti,i)=rij
+cd write (2,'(3e15.5)') rij,r0ij+0.2d0*r0ij,rij
+C --- Electrostatic-interaction matrix ---
+ a_chuj(1,1,num_conti,i)=a22
+ a_chuj(1,2,num_conti,i)=a23
+ a_chuj(2,1,num_conti,i)=a32
+ a_chuj(2,2,num_conti,i)=a33
+C --- Gradient of rij
+ do kkk=1,3
+ grij_hb_cont(kkk,num_conti,i)=erij(kkk)
+ enddo
+c if (i.eq.1) then
+c a_chuj(1,1,num_conti,i)=-0.61d0
+c a_chuj(1,2,num_conti,i)= 0.4d0
+c a_chuj(2,1,num_conti,i)= 0.65d0
+c a_chuj(2,2,num_conti,i)= 0.50d0
+c else if (i.eq.2) then
+c a_chuj(1,1,num_conti,i)= 0.0d0
+c a_chuj(1,2,num_conti,i)= 0.0d0
+c a_chuj(2,1,num_conti,i)= 0.0d0
+c a_chuj(2,2,num_conti,i)= 0.0d0
+c endif
+C --- and its gradients
+cd write (iout,*) 'i',i,' j',j
+cd do kkk=1,3
+cd write (iout,*) 'iii 1 kkk',kkk
+cd write (iout,*) agg(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 2 kkk',kkk
+cd write (iout,*) aggi(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 3 kkk',kkk
+cd write (iout,*) aggi1(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 4 kkk',kkk
+cd write (iout,*) aggj(kkk,:)
+cd enddo
+cd do kkk=1,3
+cd write (iout,*) 'iii 5 kkk',kkk
+cd write (iout,*) aggj1(kkk,:)
+cd enddo
+ kkll=0
+ do k=1,2
+ do l=1,2
+ kkll=kkll+1
+ do m=1,3
+ a_chuj_der(k,l,m,1,num_conti,i)=agg(m,kkll)
+ a_chuj_der(k,l,m,2,num_conti,i)=aggi(m,kkll)
+ a_chuj_der(k,l,m,3,num_conti,i)=aggi1(m,kkll)
+ a_chuj_der(k,l,m,4,num_conti,i)=aggj(m,kkll)
+ a_chuj_der(k,l,m,5,num_conti,i)=aggj1(m,kkll)
+c do mm=1,5
+c a_chuj_der(k,l,m,mm,num_conti,i)=0.0d0
+c enddo
+ enddo
+ enddo
+ enddo
+ ENDIF
+ IF (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) THEN
+C Calculate contact energies
+ cosa4=4.0D0*cosa
+ wij=cosa-3.0D0*cosb*cosg
+ cosbg1=cosb+cosg
+ cosbg2=cosb-cosg
+c fac3=dsqrt(-ael6i)/r0ij**3
+ fac3=dsqrt(-ael6i)*r3ij
+ ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
+ ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
+c ees0mij=0.0D0
+ ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
+ ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
+C Diagnostics. Comment out or remove after debugging!
+c ees0p(num_conti,i)=0.5D0*fac3*ees0pij
+c ees0m(num_conti,i)=0.5D0*fac3*ees0mij
+c ees0m(num_conti,i)=0.0D0
+C End diagnostics.
+c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij,
+c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont
+ facont_hb(num_conti,i)=fcont
+ if (calc_grad) then
+C Angular derivatives of the contact function
+ ees0pij1=fac3/ees0pij
+ ees0mij1=fac3/ees0mij
+ fac3p=-3.0D0*fac3*rrmij
+ ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij)
+ ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij)
+c ees0mij1=0.0D0
+ ecosa1= ees0pij1*( 1.0D0+0.5D0*wij)
+ ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1)
+ ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1)
+ ecosa2= ees0mij1*(-1.0D0+0.5D0*wij)
+ ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2)
+ ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2)
+ ecosap=ecosa1+ecosa2
+ ecosbp=ecosb1+ecosb2
+ ecosgp=ecosg1+ecosg2
+ ecosam=ecosa1-ecosa2
+ ecosbm=ecosb1-ecosb2
+ ecosgm=ecosg1-ecosg2
+C Diagnostics
+c ecosap=ecosa1
+c ecosbp=ecosb1
+c ecosgp=ecosg1
+c ecosam=0.0D0
+c ecosbm=0.0D0
+c ecosgm=0.0D0
+C End diagnostics
+ fprimcont=fprimcont/rij
+cd facont_hb(num_conti,i)=1.0D0
+C Following line is for diagnostics.
+cd fprimcont=0.0D0
+ do k=1,3
+ dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
+ dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
+ enddo
+ do k=1,3
+ gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k)
+ gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
+ enddo
+ gggp(1)=gggp(1)+ees0pijp*xj
+ gggp(2)=gggp(2)+ees0pijp*yj
+ gggp(3)=gggp(3)+ees0pijp*zj
+ gggm(1)=gggm(1)+ees0mijp*xj
+ gggm(2)=gggm(2)+ees0mijp*yj
+ gggm(3)=gggm(3)+ees0mijp*zj
+C Derivatives due to the contact function
+ gacont_hbr(1,num_conti,i)=fprimcont*xj
+ gacont_hbr(2,num_conti,i)=fprimcont*yj
+ gacont_hbr(3,num_conti,i)=fprimcont*zj
+ do k=1,3
+ ghalfp=0.5D0*gggp(k)
+ ghalfm=0.5D0*gggm(k)
+ gacontp_hb1(k,num_conti,i)=ghalfp
+ & +(ecosap*dc_norm(k,j)+ecosbp*erij(k))*vblinv
+ gacontp_hb2(k,num_conti,i)=ghalfp
+ & +(ecosap*dc_norm(k,i)+ecosgp*erij(k))*vblinv
+ gacontp_hb3(k,num_conti,i)=gggp(k)
+ gacontm_hb1(k,num_conti,i)=ghalfm
+ & +(ecosam*dc_norm(k,j)+ecosbm*erij(k))*vblinv
+ gacontm_hb2(k,num_conti,i)=ghalfm
+ & +(ecosam*dc_norm(k,i)+ecosgm*erij(k))*vblinv
+ gacontm_hb3(k,num_conti,i)=gggm(k)
+ enddo
+ endif
+C Diagnostics. Comment out or remove after debugging!
+cdiag do k=1,3
+cdiag gacontp_hb1(k,num_conti,i)=0.0D0
+cdiag gacontp_hb2(k,num_conti,i)=0.0D0
+cdiag gacontp_hb3(k,num_conti,i)=0.0D0
+cdiag gacontm_hb1(k,num_conti,i)=0.0D0
+cdiag gacontm_hb2(k,num_conti,i)=0.0D0
+cdiag gacontm_hb3(k,num_conti,i)=0.0D0
+cdiag enddo
+ ENDIF ! wcorr
+ endif ! num_conti.le.maxconts
+ endif ! fcont.gt.0
+ endif ! j.gt.i+1
+ 1216 continue
+ enddo ! j
+ num_cont_hb(i)=num_conti
+ 1215 continue
+ enddo ! i
+cd do i=1,nres
+cd write (iout,'(i3,3f10.5,5x,3f10.5)')
+cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i)
+cd enddo
+c 12/7/99 Adam eello_turn3 will be considered as a separate energy term
+ccc eel_loc=eel_loc+eello_turn3
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine eturn34(i,j,eello_turn3,eello_turn4)
+C Third- and fourth-order contributions from turns
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ include 'COMMON.FFIELD'
+ dimension ggg(3)
+ double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
+ & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
+ double precision agg(3,4),aggi(3,4),aggi1(3,4),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
+ if (j.eq.i+2) then
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Third-order contributions
+C
+C (i+2)o----(i+3)
+C | |
+C | |
+C (i+1)o----i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd call checkint_turn3(i,a_temp,eello_turn3_num)
+ call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
+ call transpose2(auxmat(1,1),auxmat1(1,1))
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+cd write (2,*) 'i,',i,' j',j,'eello_turn3',
+cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
+cd & ' eello_turn3_num',4*eello_turn3_num
+ if (calc_grad) then
+C Derivatives in gamma(i)
+ call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1))
+ call transpose2(auxmat2(1,1),pizda(1,1))
+ call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
+ gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
+C Derivatives in gamma(i+1)
+ call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
+ call transpose2(auxmat2(1,1),pizda(1,1))
+ call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
+ gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+C Cartesian derivatives
+ do l=1,3
+ a_temp(1,1)=aggi(l,1)
+ a_temp(1,2)=aggi(l,2)
+ a_temp(2,1)=aggi(l,3)
+ a_temp(2,2)=aggi(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,i)=gcorr3_turn(l,i)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggi1(l,1)
+ a_temp(1,2)=aggi1(l,2)
+ a_temp(2,1)=aggi1(l,3)
+ a_temp(2,2)=aggi1(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggj(l,1)
+ a_temp(1,2)=aggj(l,2)
+ a_temp(2,1)=aggj(l,3)
+ a_temp(2,2)=aggj(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,j)=gcorr3_turn(l,j)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ a_temp(1,1)=aggj1(l,1)
+ a_temp(1,2)=aggj1(l,2)
+ a_temp(2,1)=aggj1(l,3)
+ a_temp(2,2)=aggj1(l,4)
+ call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
+ & +0.5d0*(pizda(1,1)+pizda(2,2))
+ enddo
+ endif
+ else if (j.eq.i+3) then
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Fourth-order contributions
+C
+C (i+3)o----(i+4)
+C / |
+C (i+2)o |
+C \ |
+C (i+1)o----i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd call checkint_turn4(i,a_temp,eello_turn4_num)
+ iti1=itortyp(itype(i+1))
+ iti2=itortyp(itype(i+2))
+ iti3=itortyp(itype(i+3))
+ call transpose2(EUg(1,1,i+1),e1t(1,1))
+ call transpose2(Eug(1,1,i+2),e2t(1,1))
+ call transpose2(Eug(1,1,i+3),e3t(1,1))
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ eello_turn4=eello_turn4-(s1+s2+s3)
+cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
+cd & ' eello_turn4_num',8*eello_turn4_num
+C Derivatives in gamma(i)
+ if (calc_grad) then
+ call transpose2(EUgder(1,1,i+1),e1tder(1,1))
+ call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
+C Derivatives in gamma(i+1)
+ call transpose2(EUgder(1,1,i+2),e2tder(1,1))
+ call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1))
+ call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
+C Derivatives in gamma(i+2)
+ call transpose2(EUgder(1,1,i+3),e3tder(1,1))
+ call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1))
+ call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
+C Cartesian derivatives
+C Derivatives of this turn contributions in DC(i+2)
+ if (j.lt.nres-1) then
+ do l=1,3
+ a_temp(1,1)=agg(l,1)
+ a_temp(1,2)=agg(l,2)
+ a_temp(2,1)=agg(l,3)
+ a_temp(2,2)=agg(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ ggg(l)=-(s1+s2+s3)
+ gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
+ enddo
+ endif
+C Remaining derivatives of this turn contribution
+ do l=1,3
+ a_temp(1,1)=aggi(l,1)
+ a_temp(1,2)=aggi(l,2)
+ a_temp(2,1)=aggi(l,3)
+ a_temp(2,2)=aggi(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
+ a_temp(1,1)=aggi1(l,1)
+ a_temp(1,2)=aggi1(l,2)
+ a_temp(2,1)=aggi1(l,3)
+ a_temp(2,2)=aggi1(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
+ a_temp(1,1)=aggj(l,1)
+ a_temp(1,2)=aggj(l,2)
+ a_temp(2,1)=aggj(l,3)
+ a_temp(2,2)=aggj(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
+ a_temp(1,1)=aggj1(l,1)
+ a_temp(1,2)=aggj1(l,2)
+ a_temp(2,1)=aggj1(l,3)
+ a_temp(2,2)=aggj1(l,4)
+ call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+ call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
+ s1=scalar2(b1(1,iti2),auxvec(1))
+ call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+ call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
+ s2=scalar2(b1(1,iti1),auxvec(1))
+ call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+ call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+ s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
+ enddo
+ endif
+ endif
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine vecpr(u,v,w)
+ implicit real*8(a-h,o-z)
+ dimension u(3),v(3),w(3)
+ w(1)=u(2)*v(3)-u(3)*v(2)
+ w(2)=-u(1)*v(3)+u(3)*v(1)
+ w(3)=u(1)*v(2)-u(2)*v(1)
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine unormderiv(u,ugrad,unorm,ungrad)
+C This subroutine computes the derivatives of a normalized vector u, given
+C the derivatives computed without normalization conditions, ugrad. Returns
+C ungrad.
+ implicit none
+ double precision u(3),ugrad(3,3),unorm,ungrad(3,3)
+ double precision vec(3)
+ double precision scalar
+ integer i,j
+c write (2,*) 'ugrad',ugrad
+c write (2,*) 'u',u
+ do i=1,3
+ vec(i)=scalar(ugrad(1,i),u(1))
+ enddo
+c write (2,*) 'vec',vec
+ do i=1,3
+ do j=1,3
+ ungrad(j,i)=(ugrad(j,i)-u(j)*vec(i))*unorm
+ enddo
+ enddo
+c write (2,*) 'ungrad',ungrad
+ return
+ end
+C-----------------------------------------------------------------------------
+ subroutine escp(evdw2,evdw2_14)
+C
+C This subroutine calculates the excluded-volume interaction energy between
+C peptide-group centers and side chains and its gradient in virtual-bond and
+C side-chain vectors.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.FFIELD'
+ include 'COMMON.IOUNITS'
+ dimension ggg(3)
+ evdw2=0.0D0
+ evdw2_14=0.0d0
+cd print '(a)','Enter ESCP'
+c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
+c & ' scal14',scal14
+ do i=iatscp_s,iatscp_e
+ iteli=itel(i)
+c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
+c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
+ if (iteli.eq.0) goto 1225
+ xi=0.5D0*(c(1,i)+c(1,i+1))
+ yi=0.5D0*(c(2,i)+c(2,i+1))
+ zi=0.5D0*(c(3,i)+c(3,i+1))
+
+ do iint=1,nscp_gr(i)
+
+ do j=iscpstart(i,iint),iscpend(i,iint)
+ itypj=itype(j)
+C Uncomment following three lines for SC-p interactions
+c xj=c(1,nres+j)-xi
+c yj=c(2,nres+j)-yi
+c zj=c(3,nres+j)-zi
+C Uncomment following three lines for Ca-p interactions
+ xj=c(1,j)-xi
+ yj=c(2,j)-yi
+ zj=c(3,j)-zi
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ fac=rrij**expon2
+ e1=fac*fac*aad(itypj,iteli)
+ e2=fac*bad(itypj,iteli)
+ if (iabs(j-i) .le. 2) then
+ e1=scal14*e1
+ e2=scal14*e2
+ evdw2_14=evdw2_14+e1+e2
+ endif
+ evdwij=e1+e2
+c write (iout,*) i,j,evdwij
+ evdw2=evdw2+evdwij
+ if (calc_grad) then
+C
+C Calculate contributions to the gradient in the virtual-bond and SC vectors.
+C
+ fac=-(evdwij+e1)*rrij
+ ggg(1)=xj*fac
+ ggg(2)=yj*fac
+ ggg(3)=zj*fac
+ if (j.lt.i) then
+cd write (iout,*) 'j<i'
+C Uncomment following three lines for SC-p interactions
+c do k=1,3
+c gradx_scp(k,j)=gradx_scp(k,j)+ggg(k)
+c enddo
+ else
+cd write (iout,*) 'j>i'
+ do k=1,3
+ ggg(k)=-ggg(k)
+C Uncomment following line for SC-p interactions
+c gradx_scp(k,j)=gradx_scp(k,j)-ggg(k)
+ enddo
+ endif
+ do k=1,3
+ gvdwc_scp(k,i)=gvdwc_scp(k,i)-0.5D0*ggg(k)
+ enddo
+ kstart=min0(i+1,j)
+ kend=max0(i-1,j-1)
+cd write (iout,*) 'i=',i,' j=',j,' kstart=',kstart,' kend=',kend
+cd write (iout,*) ggg(1),ggg(2),ggg(3)
+ do k=kstart,kend
+ do l=1,3
+ gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l)
+ enddo
+ enddo
+ endif
+ enddo
+ enddo ! iint
+ 1225 continue
+ enddo ! i
+ do i=1,nct
+ do j=1,3
+ gvdwc_scp(j,i)=expon*gvdwc_scp(j,i)
+ gradx_scp(j,i)=expon*gradx_scp(j,i)
+ enddo
+ enddo
+C******************************************************************************
+C
+C N O T E !!!
+C
+C To save time the factor EXPON has been extracted from ALL components
+C of GVDWC and GRADX. Remember to multiply them by this factor before further
+C use!
+C
+C******************************************************************************
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine edis(ehpb)
+C
+C Evaluate bridge-strain energy and its gradient in virtual-bond and SC vectors.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ dimension ggg(3)
+ ehpb=0.0D0
+cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
+cd print *,'link_start=',link_start,' link_end=',link_end
+ if (link_end.eq.0) return
+ do i=link_start,link_end
+C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
+C CA-CA distance used in regularization of structure.
+ ii=ihpb(i)
+ jj=jhpb(i)
+C iii and jjj point to the residues for which the distance is assigned.
+ if (ii.gt.nres) then
+ iii=ii-nres
+ jjj=jj-nres
+ else
+ iii=ii
+ jjj=jj
+ endif
+C Calculate the distance between the two points and its difference from the
+C target distance.
+ dd=dist(ii,jj)
+ rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+ waga=forcon(i)
+C Calculate the contribution to energy.
+ ehpb=ehpb+waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+ fac=waga*rdis/dd
+cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
+cd & ' waga=',waga,' fac=',fac
+ do j=1,3
+ ggg(j)=fac*(c(j,jj)-c(j,ii))
+ enddo
+cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
+C If this is a SC-SC distace, we need to calculate the contributions to the
+C Cartesian gradient in the SC vectors (ghpbx).
+ if (iii.lt.ii) then
+ do j=1,3
+ ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+ ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+ enddo
+ endif
+ do j=iii,jjj-1
+ do k=1,3
+ ghpbc(k,j)=ghpbc(k,j)+ggg(k)
+ enddo
+ enddo
+ enddo
+ ehpb=0.5D0*ehpb
+ return
+ end
+C--------------------------------------------------------------------------
+ subroutine ebend(etheta)
+C
+C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
+C angles gamma and its derivatives in consecutive thetas and gammas.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+ double precision y(2),z(2)
+ delta=0.02d0*pi
+ time11=dexp(-2*time)
+ time12=1.0d0
+ etheta=0.0D0
+c write (iout,*) "nres",nres
+c write (*,'(a,i2)') 'EBEND ICG=',icg
+c write (iout,*) ithet_start,ithet_end
+ do i=ithet_start,ithet_end
+C Zero the energy function and its derivative at 0 or pi.
+ call splinthet(theta(i),0.5d0*delta,ss,ssd)
+ it=itype(i-1)
+ if (i.gt.ithet_start .and.
+ & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
+ if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
+ phii=phi(i)
+ y(1)=dcos(phii)
+ y(2)=dsin(phii)
+ else
+ y(1)=0.0D0
+ y(2)=0.0D0
+ endif
+ if (i.lt.nres .and. itel(i).ne.0) then
+ phii1=phi(i+1)
+ z(1)=dcos(phii1)
+ z(2)=dsin(phii1)
+ else
+ z(1)=0.0D0
+ z(2)=0.0D0
+ endif
+C Calculate the "mean" value of theta from the part of the distribution
+C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2).
+C In following comments this theta will be referred to as t_c.
+ thet_pred_mean=0.0d0
+ do k=1,2
+ athetk=athet(k,it)
+ bthetk=bthet(k,it)
+ thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
+ enddo
+c write (iout,*) "thet_pred_mean",thet_pred_mean
+ dthett=thet_pred_mean*ssd
+ thet_pred_mean=thet_pred_mean*ss+a0thet(it)
+c write (iout,*) "thet_pred_mean",thet_pred_mean
+C Derivatives of the "mean" values in gamma1 and gamma2.
+ dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
+ dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ if (theta(i).gt.pi-delta) then
+ call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
+ & E_tc0)
+ call mixder(pi-delta,thet_pred_mean,theta0(it),fprim_tc0)
+ call theteng(pi,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
+ call spline1(theta(i),pi-delta,delta,f0,f1,fprim0,ethetai,
+ & E_theta)
+ call spline2(theta(i),pi-delta,delta,E_tc0,E_tc1,fprim_tc0,
+ & E_tc)
+ else if (theta(i).lt.delta) then
+ call theteng(delta,thet_pred_mean,theta0(it),f0,fprim0,E_tc0)
+ call theteng(0.0d0,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
+ call spline1(theta(i),delta,-delta,f0,f1,fprim0,ethetai,
+ & E_theta)
+ call mixder(delta,thet_pred_mean,theta0(it),fprim_tc0)
+ call spline2(theta(i),delta,-delta,E_tc0,E_tc1,fprim_tc0,
+ & E_tc)
+ else
+ call theteng(theta(i),thet_pred_mean,theta0(it),ethetai,
+ & E_theta,E_tc)
+ endif
+ etheta=etheta+ethetai
+c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i),
+c & rad2deg*phii,rad2deg*phii1,ethetai
+ if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
+ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
+ gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
+ 1215 continue
+ enddo
+C Ufff.... We've done all this!!!
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine theteng(thetai,thet_pred_mean,theta0i,ethetai,E_theta,
+ & E_tc)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+C Calculate the contributions to both Gaussian lobes.
+C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time)
+C The "polynomial part" of the "standard deviation" of this part of
+C the distribution.
+ sig=polthet(3,it)
+ do j=2,0,-1
+ sig=sig*thet_pred_mean+polthet(j,it)
+ enddo
+C Derivative of the "interior part" of the "standard deviation of the"
+C gamma-dependent Gaussian lobe in t_c.
+ sigtc=3*polthet(3,it)
+ do j=2,1,-1
+ sigtc=sigtc*thet_pred_mean+j*polthet(j,it)
+ enddo
+ sigtc=sig*sigtc
+C Set the parameters of both Gaussian lobes of the distribution.
+C "Standard deviation" of the gamma-dependent Gaussian lobe (sigtc)
+ fac=sig*sig+sigc0(it)
+ sigcsq=fac+fac
+ sigc=1.0D0/sigcsq
+C Following variable (sigsqtc) is -(1/2)d[sigma(t_c)**(-2))]/dt_c
+ sigsqtc=-4.0D0*sigcsq*sigtc
+c print *,i,sig,sigtc,sigsqtc
+C Following variable (sigtc) is d[sigma(t_c)]/dt_c
+ sigtc=-sigtc/(fac*fac)
+C Following variable is sigma(t_c)**(-2)
+ sigcsq=sigcsq*sigcsq
+ sig0i=sig0(it)
+ sig0inv=1.0D0/sig0i**2
+ delthec=thetai-thet_pred_mean
+ delthe0=thetai-theta0i
+ term1=-0.5D0*sigcsq*delthec*delthec
+ term2=-0.5D0*sig0inv*delthe0*delthe0
+C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and
+C NaNs in taking the logarithm. We extract the largest exponent which is added
+C to the energy (this being the log of the distribution) at the end of energy
+C term evaluation for this virtual-bond angle.
+ if (term1.gt.term2) then
+ termm=term1
+ term2=dexp(term2-termm)
+ term1=1.0d0
+ else
+ termm=term2
+ term1=dexp(term1-termm)
+ term2=1.0d0
+ endif
+C The ratio between the gamma-independent and gamma-dependent lobes of
+C the distribution is a Gaussian function of thet_pred_mean too.
+ diffak=gthet(2,it)-thet_pred_mean
+ ratak=diffak/gthet(3,it)**2
+ ak=dexp(gthet(1,it)-0.5D0*diffak*ratak)
+C Let's differentiate it in thet_pred_mean NOW.
+ aktc=ak*ratak
+C Now put together the distribution terms to make complete distribution.
+ termexp=term1+ak*term2
+ termpre=sigc+ak*sig0i
+C Contribution of the bending energy from this theta is just the -log of
+C the sum of the contributions from the two lobes and the pre-exponential
+C factor. Simple enough, isn't it?
+ ethetai=(-dlog(termexp)-termm+dlog(termpre))
+C NOW the derivatives!!!
+C 6/6/97 Take into account the deformation.
+ E_theta=(delthec*sigcsq*term1
+ & +ak*delthe0*sig0inv*term2)/termexp
+ E_tc=((sigtc+aktc*sig0i)/termpre
+ & -((delthec*sigcsq+delthec*delthec*sigsqtc)*term1+
+ & aktc*term2)/termexp)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine mixder(thetai,thet_pred_mean,theta0i,E_tc_t)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /calcthet/ term1,term2,termm,diffak,ratak,
+ & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
+ & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
+ delthec=thetai-thet_pred_mean
+ delthe0=thetai-theta0i
+C "Thank you" to MAPLE (probably spared one day of hand-differentiation).
+ t3 = thetai-thet_pred_mean
+ t6 = t3**2
+ t9 = term1
+ t12 = t3*sigcsq
+ t14 = t12+t6*sigsqtc
+ t16 = 1.0d0
+ t21 = thetai-theta0i
+ t23 = t21**2
+ t26 = term2
+ t27 = t21*t26
+ t32 = termexp
+ t40 = t32**2
+ E_tc_t = -((sigcsq+2.D0*t3*sigsqtc)*t9-t14*sigcsq*t3*t16*t9
+ & -aktc*sig0inv*t27)/t32+(t14*t9+aktc*t26)/t40
+ & *(-t12*t9-ak*sig0inv*t27)
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine esc(escloc)
+C Calculate the local energy of a side chain and its derivatives in the
+C corresponding virtual-bond valence angles THETA and the spherical angles
+C ALPHA and OMEGA.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ double precision x(3),dersc(3),xemp(3),dersc0(3),dersc1(3),
+ & ddersc0(3),ddummy(3),xtemp(3),temp(3)
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ delta=0.02d0*pi
+ escloc=0.0D0
+c write (iout,'(a)') 'ESC'
+ do i=loc_start,loc_end
+ it=itype(i)
+ if (it.eq.10) goto 1
+ nlobit=nlob(it)
+c print *,'i=',i,' it=',it,' nlobit=',nlobit
+c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
+ theti=theta(i+1)-pipol
+ x(1)=dtan(theti)
+ x(2)=alph(i)
+ x(3)=omeg(i)
+
+ if (x(2).gt.pi-delta) then
+ xtemp(1)=x(1)
+ xtemp(2)=pi-delta
+ xtemp(3)=x(3)
+ call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
+ xtemp(2)=pi
+ call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
+ call spline1(x(2),pi-delta,delta,escloci0,escloci1,dersc0(2),
+ & escloci,dersc(2))
+ call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
+ & ddersc0(1),dersc(1))
+ call spline2(x(2),pi-delta,delta,dersc0(3),dersc1(3),
+ & ddersc0(3),dersc(3))
+ xtemp(2)=pi-delta
+ call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
+ xtemp(2)=pi
+ call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
+ call spline1(x(2),pi-delta,delta,esclocbi0,esclocbi1,
+ & dersc0(2),esclocbi,dersc02)
+ call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
+ & dersc12,dersc01)
+ call splinthet(x(2),0.5d0*delta,ss,ssd)
+ dersc0(1)=dersc01
+ dersc0(2)=dersc02
+ dersc0(3)=0.0d0
+ do k=1,3
+ dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
+ enddo
+ dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
+c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
+c & esclocbi,ss,ssd
+ escloci=ss*escloci+(1.0d0-ss)*esclocbi
+c escloci=esclocbi
+c write (iout,*) escloci
+ else if (x(2).lt.delta) then
+ xtemp(1)=x(1)
+ xtemp(2)=delta
+ xtemp(3)=x(3)
+ call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
+ xtemp(2)=0.0d0
+ call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
+ call spline1(x(2),delta,-delta,escloci0,escloci1,dersc0(2),
+ & escloci,dersc(2))
+ call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
+ & ddersc0(1),dersc(1))
+ call spline2(x(2),delta,-delta,dersc0(3),dersc1(3),
+ & ddersc0(3),dersc(3))
+ xtemp(2)=delta
+ call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
+ xtemp(2)=0.0d0
+ call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
+ call spline1(x(2),delta,-delta,esclocbi0,esclocbi1,
+ & dersc0(2),esclocbi,dersc02)
+ call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
+ & dersc12,dersc01)
+ dersc0(1)=dersc01
+ dersc0(2)=dersc02
+ dersc0(3)=0.0d0
+ call splinthet(x(2),0.5d0*delta,ss,ssd)
+ do k=1,3
+ dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
+ enddo
+ dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
+c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
+c & esclocbi,ss,ssd
+ escloci=ss*escloci+(1.0d0-ss)*esclocbi
+c write (iout,*) escloci
+ else
+ call enesc(x,escloci,dersc,ddummy,.false.)
+ endif
+
+ escloc=escloc+escloci
+c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
+
+ gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
+ & wscloc*dersc(1)
+ gloc(ialph(i,1),icg)=wscloc*dersc(2)
+ gloc(ialph(i,1)+nside,icg)=wscloc*dersc(3)
+ 1 continue
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine enesc(x,escloci,dersc,ddersc,mixed)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ double precision x(3),z(3),Ax(3,maxlob,-1:1),dersc(3),ddersc(3)
+ double precision contr(maxlob,-1:1)
+ logical mixed
+c write (iout,*) 'it=',it,' nlobit=',nlobit
+ escloc_i=0.0D0
+ do j=1,3
+ dersc(j)=0.0D0
+ if (mixed) ddersc(j)=0.0d0
+ enddo
+ x3=x(3)
+
+C Because of periodicity of the dependence of the SC energy in omega we have
+C to add up the contributions from x(3)-2*pi, x(3), and x(3+2*pi).
+C To avoid underflows, first compute & store the exponents.
+
+ do iii=-1,1
+
+ x(3)=x3+iii*dwapi
+
+ do j=1,nlobit
+ do k=1,3
+ z(k)=x(k)-censc(k,j,it)
+ enddo
+ do k=1,3
+ Axk=0.0D0
+ do l=1,3
+ Axk=Axk+gaussc(l,k,j,it)*z(l)
+ enddo
+ Ax(k,j,iii)=Axk
+ enddo
+ expfac=0.0D0
+ do k=1,3
+ expfac=expfac+Ax(k,j,iii)*z(k)
+ enddo
+ contr(j,iii)=expfac
+ enddo ! j
+
+ enddo ! iii
+
+ x(3)=x3
+C As in the case of ebend, we want to avoid underflows in exponentiation and
+C subsequent NaNs and INFs in energy calculation.
+C Find the largest exponent
+ emin=contr(1,-1)
+ do iii=-1,1
+ do j=1,nlobit
+ if (emin.gt.contr(j,iii)) emin=contr(j,iii)
+ enddo
+ enddo
+ emin=0.5D0*emin
+cd print *,'it=',it,' emin=',emin
+
+C Compute the contribution to SC energy and derivatives
+ do iii=-1,1
+
+ do j=1,nlobit
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+cd print *,'j=',j,' expfac=',expfac
+ escloc_i=escloc_i+expfac
+ do k=1,3
+ dersc(k)=dersc(k)+Ax(k,j,iii)*expfac
+ enddo
+ if (mixed) then
+ do k=1,3,2
+ ddersc(k)=ddersc(k)+(-Ax(2,j,iii)*Ax(k,j,iii)
+ & +gaussc(k,2,j,it))*expfac
+ enddo
+ endif
+ enddo
+
+ enddo ! iii
+
+ dersc(1)=dersc(1)/cos(theti)**2
+ ddersc(1)=ddersc(1)/cos(theti)**2
+ ddersc(3)=ddersc(3)
+
+ escloci=-(dlog(escloc_i)-emin)
+ do j=1,3
+ dersc(j)=dersc(j)/escloc_i
+ enddo
+ if (mixed) then
+ do j=1,3,2
+ ddersc(j)=(ddersc(j)/escloc_i+dersc(2)*dersc(j))
+ enddo
+ endif
+ return
+ end
+C------------------------------------------------------------------------------
+ subroutine enesc_bound(x,escloci,dersc,dersc12,mixed)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.IOUNITS'
+ common /sccalc/ time11,time12,time112,theti,it,nlobit
+ double precision x(3),z(3),Ax(3,maxlob),dersc(3)
+ double precision contr(maxlob)
+ logical mixed
+
+ escloc_i=0.0D0
+
+ do j=1,3
+ dersc(j)=0.0D0
+ enddo
+
+ do j=1,nlobit
+ do k=1,2
+ z(k)=x(k)-censc(k,j,it)
+ enddo
+ z(3)=dwapi
+ do k=1,3
+ Axk=0.0D0
+ do l=1,3
+ Axk=Axk+gaussc(l,k,j,it)*z(l)
+ enddo
+ Ax(k,j)=Axk
+ enddo
+ expfac=0.0D0
+ do k=1,3
+ expfac=expfac+Ax(k,j)*z(k)
+ enddo
+ contr(j)=expfac
+ enddo ! j
+
+C As in the case of ebend, we want to avoid underflows in exponentiation and
+C subsequent NaNs and INFs in energy calculation.
+C Find the largest exponent
+ emin=contr(1)
+ do j=1,nlobit
+ if (emin.gt.contr(j)) emin=contr(j)
+ enddo
+ emin=0.5D0*emin
+
+C Compute the contribution to SC energy and derivatives
+
+ dersc12=0.0d0
+ do j=1,nlobit
+ expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ escloc_i=escloc_i+expfac
+ do k=1,2
+ dersc(k)=dersc(k)+Ax(k,j)*expfac
+ enddo
+ if (mixed) dersc12=dersc12+(-Ax(2,j)*Ax(1,j)
+ & +gaussc(1,2,j,it))*expfac
+ dersc(3)=0.0d0
+ enddo
+
+ dersc(1)=dersc(1)/cos(theti)**2
+ dersc12=dersc12/cos(theti)**2
+ escloci=-(dlog(escloc_i)-emin)
+ do j=1,2
+ dersc(j)=dersc(j)/escloc_i
+ enddo
+ if (mixed) dersc12=(dersc12/escloc_i+dersc(2)*dersc(1))
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine gcont(rij,r0ij,eps0ij,delta,fcont,fprimcont)
+C
+C This procedure calculates two-body contact function g(rij) and its derivative:
+C
+C eps0ij ! x < -1
+C g(rij) = esp0ij*(-0.9375*x+0.625*x**3-0.1875*x**5) ! -1 =< x =< 1
+C 0 ! x > 1
+C
+C where x=(rij-r0ij)/delta
+C
+C rij - interbody distance, r0ij - contact distance, eps0ij - contact energy
+C
+ implicit none
+ double precision rij,r0ij,eps0ij,fcont,fprimcont
+ double precision x,x2,x4,delta
+c delta=0.02D0*r0ij
+c delta=0.2D0*r0ij
+ x=(rij-r0ij)/delta
+ if (x.lt.-1.0D0) then
+ fcont=eps0ij
+ fprimcont=0.0D0
+ else if (x.le.1.0D0) then
+ x2=x*x
+ x4=x2*x2
+ fcont=eps0ij*(x*(-0.9375D0+0.6250D0*x2-0.1875D0*x4)+0.5D0)
+ fprimcont=eps0ij * (-0.9375D0+1.8750D0*x2-0.9375D0*x4)/delta
+ else
+ fcont=0.0D0
+ fprimcont=0.0D0
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine splinthet(theti,delta,ss,ssder)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ thetup=pi-delta
+ thetlow=delta
+ if (theti.gt.pipol) then
+ call gcont(theti,thetup,1.0d0,delta,ss,ssder)
+ else
+ call gcont(-theti,-thetlow,1.0d0,delta,ss,ssder)
+ ssder=-ssder
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine spline1(x,x0,delta,f0,f1,fprim0,f,fprim)
+ implicit none
+ double precision x,x0,delta,f0,f1,fprim0,f,fprim
+ double precision ksi,ksi2,ksi3,a1,a2,a3
+ a1=fprim0*delta/(f1-f0)
+ a2=3.0d0-2.0d0*a1
+ a3=a1-2.0d0
+ ksi=(x-x0)/delta
+ ksi2=ksi*ksi
+ ksi3=ksi2*ksi
+ f=f0+(f1-f0)*ksi*(a1+ksi*(a2+a3*ksi))
+ fprim=(f1-f0)/delta*(a1+ksi*(2*a2+3*ksi*a3))
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine spline2(x,x0,delta,f0x,f1x,fprim0x,fx)
+ implicit none
+ double precision x,x0,delta,f0x,f1x,fprim0x,fx
+ double precision ksi,ksi2,ksi3,a1,a2,a3
+ ksi=(x-x0)/delta
+ ksi2=ksi*ksi
+ ksi3=ksi2*ksi
+ a1=fprim0x*delta
+ a2=3*(f1x-f0x)-2*fprim0x*delta
+ a3=fprim0x*delta-2*(f1x-f0x)
+ fx=f0x+a1*ksi+a2*ksi2+a3*ksi3
+ return
+ end
+C-----------------------------------------------------------------------------
+#ifdef CRYST_TOR
+C-----------------------------------------------------------------------------
+ subroutine etor(etors,edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ gloci=0.0D0
+C Proline-Proline pair is a special case...
+ if (itori.eq.3 .and. itori1.eq.3) then
+ if (phii.gt.-dwapi3) then
+ cosphi=dcos(3*phii)
+ fac=1.0D0/(1.0D0-cosphi)
+ etorsi=v1(1,3,3)*fac
+ etorsi=etorsi+etorsi
+ etors=etors+etorsi-v1(1,3,3)
+ gloci=gloci-3*fac*etorsi*dsin(3*phii)
+ endif
+ do j=1,3
+ v1ij=v1(j+1,itori,itori1)
+ v2ij=v2(j+1,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+ else
+ do j=1,nterm_old
+ v1ij=v1(j,itori,itori1)
+ v2ij=v2(j,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+ endif
+ if (lprn)
+ & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
+ & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
+c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
+ enddo
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+ do i=1,ndih_constr
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=phii-phi0(i)
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ endif
+! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
+! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+ enddo
+! write (iout,*) 'edihcnstr',edihcnstr
+ return
+ end
+c------------------------------------------------------------------------------
+#else
+ subroutine etor(etors,edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+ if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ gloci=0.0D0
+C Regular cosine and sine terms
+ do j=1,nterm(itori,itori1)
+ v1ij=v1(j,itori,itori1)
+ v2ij=v2(j,itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ etors=etors+v1ij*cosphi+v2ij*sinphi
+ gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
+ enddo
+C Lorentz terms
+C v1
+C E = SUM ----------------------------------- - v1
+C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
+C
+ cosphi=dcos(0.5d0*phii)
+ sinphi=dsin(0.5d0*phii)
+ do j=1,nlor(itori,itori1)
+ vl1ij=vlor1(j,itori,itori1)
+ vl2ij=vlor2(j,itori,itori1)
+ vl3ij=vlor3(j,itori,itori1)
+ pom=vl2ij*cosphi+vl3ij*sinphi
+ pom1=1.0d0/(pom*pom+1.0d0)
+ etors=etors+vl1ij*pom1
+ pom=-pom*pom1*pom1
+ gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
+ enddo
+C Subtract the constant term
+ etors=etors-v0(itori,itori1)
+ if (lprn)
+ & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
+ & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
+ & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
+c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
+ 1215 continue
+ enddo
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+ do i=1,ndih_constr
+ print *,"i",i
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=phii-phi0(i)
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ else if (difi.lt.-drange(i)) then
+ difi=difi+drange(i)
+ edihcnstr=edihcnstr+0.25d0*ftors*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
+ endif
+! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
+! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+ enddo
+! write (iout,*) 'edihcnstr',edihcnstr
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine etor_d(etors_d)
+C 6/23/01 Compute double torsional energy
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ logical lprn
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors_d=0.0D0
+ do i=iphi_start,iphi_end-1
+ if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
+ & goto 1215
+ itori=itortyp(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ itori2=itortyp(itype(i))
+ phii=phi(i)
+ phii1=phi(i+1)
+ gloci1=0.0D0
+ gloci2=0.0D0
+C Regular cosine and sine terms
+ do j=1,ntermd_1(itori,itori1,itori2)
+ v1cij=v1c(1,j,itori,itori1,itori2)
+ v1sij=v1s(1,j,itori,itori1,itori2)
+ v2cij=v1c(2,j,itori,itori1,itori2)
+ v2sij=v1s(2,j,itori,itori1,itori2)
+ cosphi1=dcos(j*phii)
+ sinphi1=dsin(j*phii)
+ cosphi2=dcos(j*phii1)
+ sinphi2=dsin(j*phii1)
+ etors_d=etors_d+v1cij*cosphi1+v1sij*sinphi1+
+ & v2cij*cosphi2+v2sij*sinphi2
+ gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
+ gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
+ enddo
+ do k=2,ntermd_2(itori,itori1,itori2)
+ do l=1,k-1
+ v1cdij = v2c(k,l,itori,itori1,itori2)
+ v2cdij = v2c(l,k,itori,itori1,itori2)
+ v1sdij = v2s(k,l,itori,itori1,itori2)
+ v2sdij = v2s(l,k,itori,itori1,itori2)
+ cosphi1p2=dcos(l*phii+(k-l)*phii1)
+ cosphi1m2=dcos(l*phii-(k-l)*phii1)
+ sinphi1p2=dsin(l*phii+(k-l)*phii1)
+ sinphi1m2=dsin(l*phii-(k-l)*phii1)
+ etors_d=etors_d+v1cdij*cosphi1p2+v2cdij*cosphi1m2+
+ & v1sdij*sinphi1p2+v2sdij*sinphi1m2
+ gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
+ & -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
+ gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
+ & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
+ enddo
+ enddo
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1
+ gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2
+ 1215 continue
+ enddo
+ return
+ end
+#endif
+c------------------------------------------------------------------------------
+ subroutine multibody(ecorr)
+C This subroutine calculates multi-body contributions to energy following
+C the idea of Skolnick et al. If side chains I and J make a contact and
+C at the same time side chains I+1 and J+1 make a contact, an extra
+C contribution equal to sqrt(eps(i,j)*eps(i+1,j+1)) is added.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(i2,20(1x,i2,f10.5))')
+ & i,(jcont(j,i),facont(j,i),j=1,num_cont(i))
+ enddo
+ endif
+ ecorr=0.0D0
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+ do i=nnt,nct-2
+
+ DO ISHIFT = 3,4
+
+ i1=i+ishift
+ num_conti=num_cont(i)
+ num_conti1=num_cont(i1)
+ do jj=1,num_conti
+ j=jcont(jj,i)
+ do kk=1,num_conti1
+ j1=jcont(kk,i1)
+ if (j1.eq.j+ishift .or. j1.eq.j-ishift) then
+cd write(iout,*)'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+cd & ' ishift=',ishift
+C Contacts I--J and I+ISHIFT--J+-ISHIFT1 occur simultaneously.
+C The system gains extra energy.
+ ecorr=ecorr+esccorr(i,j,i1,j1,jj,kk)
+ endif ! j1==j+-ishift
+ enddo ! kk
+ enddo ! jj
+
+ ENDDO ! ISHIFT
+
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function esccorr(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+ lprn=.false.
+ eij=facont(jj,i)
+ ekl=facont(kk,k)
+cd write (iout,'(4i5,3f10.5)') i,j,k,l,eij,ekl,-eij*ekl
+C Calculate the multi-body contribution to energy.
+C Calculate multi-body contributions to the gradient.
+cd write (iout,'(2(2i3,3f10.5))')i,j,(gacont(m,jj,i),m=1,3),
+cd & k,l,(gacont(m,kk,k),m=1,3)
+ do m=1,3
+ gx(m) =ekl*gacont(m,jj,i)
+ gx1(m)=eij*gacont(m,kk,k)
+ gradxorr(m,i)=gradxorr(m,i)-gx(m)
+ gradxorr(m,j)=gradxorr(m,j)+gx(m)
+ gradxorr(m,k)=gradxorr(m,k)-gx1(m)
+ gradxorr(m,l)=gradxorr(m,l)+gx1(m)
+ enddo
+ do m=i,j-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+gx(ll)
+ enddo
+ enddo
+ do m=k,l-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+gx1(ll)
+ enddo
+ enddo
+ esccorr=-eij*ekl
+ return
+ end
+c------------------------------------------------------------------------------
+#ifdef MPL
+ subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ integer dimen1,dimen2,atom,indx
+ double precision buffer(dimen1,dimen2)
+ double precision zapas
+ common /contacts_hb/ zapas(3,20,maxres,7),
+ & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
+ & num_cont_hb(maxres),jcont_hb(20,maxres)
+ num_kont=num_cont_hb(atom)
+ do i=1,num_kont
+ do k=1,7
+ do j=1,3
+ buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k)
+ enddo ! j
+ enddo ! k
+ buffer(i,indx+22)=facont_hb(i,atom)
+ buffer(i,indx+23)=ees0p(i,atom)
+ buffer(i,indx+24)=ees0m(i,atom)
+ buffer(i,indx+25)=dfloat(jcont_hb(i,atom))
+ enddo ! i
+ buffer(1,indx+26)=dfloat(num_kont)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ integer dimen1,dimen2,atom,indx
+ double precision buffer(dimen1,dimen2)
+ double precision zapas
+ common /contacts_hb/ zapas(3,20,maxres,7),
+ & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
+ & num_cont_hb(maxres),jcont_hb(20,maxres)
+ num_kont=buffer(1,indx+26)
+ num_kont_old=num_cont_hb(atom)
+ num_cont_hb(atom)=num_kont+num_kont_old
+ do i=1,num_kont
+ ii=i+num_kont_old
+ do k=1,7
+ do j=1,3
+ zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
+ enddo ! j
+ enddo ! k
+ facont_hb(ii,atom)=buffer(i,indx+22)
+ ees0p(ii,atom)=buffer(i,indx+23)
+ ees0m(ii,atom)=buffer(i,indx+24)
+ jcont_hb(ii,atom)=buffer(i,indx+25)
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+#endif
+ subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
+C This subroutine calculates multi-body contributions to hydrogen-bonding
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+#ifdef MPL
+ parameter (max_cont=maxconts)
+ parameter (max_dim=2*(8*3+2))
+ parameter (msglen1=max_cont*max_dim*4)
+ parameter (msglen2=2*msglen1)
+ integer source,CorrelType,CorrelID,Error
+ double precision buffer(max_cont,max_dim)
+#endif
+ double precision gx(3),gx1(3)
+ logical lprn,ldone
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+#ifdef MPL
+ n_corr=0
+ n_corr1=0
+ if (fgProcs.le.1) goto 30
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+C Caution! Following code assumes that electrostatic interactions concerning
+C a given atom are split among at most two processors!
+ CorrelType=477
+ CorrelID=MyID+1
+ ldone=.false.
+ do i=1,max_cont
+ do j=1,max_dim
+ buffer(i,j)=0.0D0
+ enddo
+ enddo
+ mm=mod(MyRank,2)
+cd write (iout,*) 'MyRank',MyRank,' mm',mm
+ if (mm) 20,20,10
+ 10 continue
+cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.gt.0) then
+C Send correlation contributions to the preceding processor
+ msglen=msglen1
+ nn=num_cont_hb(iatel_s)
+ call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
+cd write (iout,*) 'The BUFFER array:'
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
+cd enddo
+ if (ielstart(iatel_s).gt.iatel_s+ispp) then
+ msglen=msglen2
+ call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
+C Clear the contacts of the atom passed to the neighboring processor
+ nn=num_cont_hb(iatel_s+1)
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
+cd enddo
+ num_cont_hb(iatel_s)=0
+ endif
+cd write (iout,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen
+cd write (*,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
+cd write (iout,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+cd write (*,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+ msglen=msglen1
+ endif ! (MyRank.gt.0)
+ if (ldone) goto 30
+ ldone=.true.
+ 20 continue
+cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.lt.fgProcs-1) then
+C Receive correlation contributions from the next processor
+ msglen=msglen1
+ if (ielend(iatel_e).lt.nct-1) msglen=msglen2
+cd write (iout,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+cd write (*,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ nbytes=-1
+ do while (nbytes.le.0)
+ call mp_probe(MyID+1,CorrelType,nbytes)
+ enddo
+cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
+ call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
+cd write (iout,*) 'Processor',MyID,
+cd & ' has received correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' nbytes=',nbytes
+cd write (iout,*) 'The received BUFFER array:'
+cd do i=1,max_cont
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
+cd enddo
+ if (msglen.eq.msglen1) then
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
+ else if (msglen.eq.msglen2) then
+ call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
+ else
+ write (iout,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ write (*,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ call mp_stopall(Error)
+ endif ! msglen.eq.msglen1
+ endif ! MyRank.lt.fgProcs-1
+ if (ldone) goto 30
+ ldone=.true.
+ goto 10
+ 30 continue
+#endif
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+ ecorr=0.0D0
+C Remove the loop below after debugging !!!
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+C Calculate the local-electrostatic correlation terms
+ do i=iatel_s,iatel_e+1
+ i1=i+1
+ num_conti=num_cont_hb(i)
+ num_conti1=num_cont_hb(i+1)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ do kk=1,num_conti1
+ j1=jcont_hb(kk,i1)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1 .or. j1.eq.j-1) then
+C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
+C The system gains extra energy.
+ ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
+ n_corr=n_corr+1
+ else if (j1.eq.j) then
+C Contacts I-J and I-(J+1) occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
+ endif
+ enddo ! kk
+ do kk=1,num_conti
+ j1=jcont_hb(kk,i)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1) then
+C Contacts I-J and (I+1)-J occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
+ endif ! j1==j+1
+ enddo ! kk
+ enddo ! jj
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,
+ & n_corr1)
+C This subroutine calculates multi-body contributions to hydrogen-bonding
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+#ifdef MPL
+ parameter (max_cont=maxconts)
+ parameter (max_dim=2*(8*3+2))
+ parameter (msglen1=max_cont*max_dim*4)
+ parameter (msglen2=2*msglen1)
+ integer source,CorrelType,CorrelID,Error
+ double precision buffer(max_cont,max_dim)
+#endif
+ double precision gx(3),gx1(3)
+ logical lprn,ldone
+
+C Set lprn=.true. for debugging
+ lprn=.false.
+ eturn6=0.0d0
+#ifdef MPL
+ n_corr=0
+ n_corr1=0
+ if (fgProcs.le.1) goto 30
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+C Caution! Following code assumes that electrostatic interactions concerning
+C a given atom are split among at most two processors!
+ CorrelType=477
+ CorrelID=MyID+1
+ ldone=.false.
+ do i=1,max_cont
+ do j=1,max_dim
+ buffer(i,j)=0.0D0
+ enddo
+ enddo
+ mm=mod(MyRank,2)
+cd write (iout,*) 'MyRank',MyRank,' mm',mm
+ if (mm) 20,20,10
+ 10 continue
+cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.gt.0) then
+C Send correlation contributions to the preceding processor
+ msglen=msglen1
+ nn=num_cont_hb(iatel_s)
+ call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
+cd write (iout,*) 'The BUFFER array:'
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
+cd enddo
+ if (ielstart(iatel_s).gt.iatel_s+ispp) then
+ msglen=msglen2
+ call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
+C Clear the contacts of the atom passed to the neighboring processor
+ nn=num_cont_hb(iatel_s+1)
+cd do i=1,nn
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
+cd enddo
+ num_cont_hb(iatel_s)=0
+ endif
+cd write (iout,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen
+cd write (*,*) 'Processor ',MyID,MyRank,
+cd & ' is sending correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
+cd write (iout,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+cd write (*,*) 'Processor ',MyID,
+cd & ' has sent correlation contribution to processor',MyID-1,
+cd & ' msglen=',msglen,' CorrelID=',CorrelID
+ msglen=msglen1
+ endif ! (MyRank.gt.0)
+ if (ldone) goto 30
+ ldone=.true.
+ 20 continue
+cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
+ if (MyRank.lt.fgProcs-1) then
+C Receive correlation contributions from the next processor
+ msglen=msglen1
+ if (ielend(iatel_e).lt.nct-1) msglen=msglen2
+cd write (iout,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+cd write (*,*) 'Processor',MyID,
+cd & ' is receiving correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' CorrelType=',CorrelType
+ nbytes=-1
+ do while (nbytes.le.0)
+ call mp_probe(MyID+1,CorrelType,nbytes)
+ enddo
+cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
+ call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
+cd write (iout,*) 'Processor',MyID,
+cd & ' has received correlation contribution from processor',MyID+1,
+cd & ' msglen=',msglen,' nbytes=',nbytes
+cd write (iout,*) 'The received BUFFER array:'
+cd do i=1,max_cont
+cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
+cd enddo
+ if (msglen.eq.msglen1) then
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
+ else if (msglen.eq.msglen2) then
+ call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
+ call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
+ else
+ write (iout,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ write (*,*)
+ & 'ERROR!!!! message length changed while processing correlations.'
+ call mp_stopall(Error)
+ endif ! msglen.eq.msglen1
+ endif ! MyRank.lt.fgProcs-1
+ if (ldone) goto 30
+ ldone=.true.
+ goto 10
+ 30 continue
+#endif
+ if (lprn) then
+ write (iout,'(a)') 'Contact function values:'
+ do i=nnt,nct-2
+ write (iout,'(2i3,50(1x,i2,f5.2))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
+ & j=1,num_cont_hb(i))
+ enddo
+ endif
+ ecorr=0.0D0
+ ecorr5=0.0d0
+ ecorr6=0.0d0
+C Remove the loop below after debugging !!!
+ do i=nnt,nct
+ do j=1,3
+ gradcorr(j,i)=0.0D0
+ gradxorr(j,i)=0.0D0
+ enddo
+ enddo
+C Calculate the dipole-dipole interaction energies
+ if (wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) then
+ do i=iatel_s,iatel_e+1
+ num_conti=num_cont_hb(i)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ call dipole(i,j,jj)
+ enddo
+ enddo
+ endif
+C Calculate the local-electrostatic correlation terms
+ do i=iatel_s,iatel_e+1
+ i1=i+1
+ num_conti=num_cont_hb(i)
+ num_conti1=num_cont_hb(i+1)
+ do jj=1,num_conti
+ j=jcont_hb(jj,i)
+ do kk=1,num_conti1
+ j1=jcont_hb(kk,i1)
+c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1 .or. j1.eq.j-1) then
+C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
+C The system gains extra energy.
+ n_corr=n_corr+1
+ sqd1=dsqrt(d_cont(jj,i))
+ sqd2=dsqrt(d_cont(kk,i1))
+ sred_geom = sqd1*sqd2
+ IF (sred_geom.lt.cutoff_corr) THEN
+ call gcont(sred_geom,r0_corr,1.0D0,delt_corr,
+ & ekont,fprimcont)
+c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ fac_prim1=0.5d0*sqd2/sqd1*fprimcont
+ fac_prim2=0.5d0*sqd1/sqd2*fprimcont
+ do l=1,3
+ g_contij(l,1)=fac_prim1*grij_hb_cont(l,jj,i)
+ g_contij(l,2)=fac_prim2*grij_hb_cont(l,kk,i1)
+ enddo
+ n_corr1=n_corr1+1
+cd write (iout,*) 'sred_geom=',sred_geom,
+cd & ' ekont=',ekont,' fprim=',fprimcont
+ call calc_eello(i,j,i+1,j1,jj,kk)
+ if (wcorr4.gt.0.0d0)
+ & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk)
+ if (wcorr5.gt.0.0d0)
+ & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk)
+c print *,"wcorr5",ecorr5
+cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6
+cd write(2,*)'ijkl',i,j,i+1,j1
+ if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
+ & .or. wturn6.eq.0.0d0))then
+cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
+ ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
+cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
+cd & 'ecorr6=',ecorr6
+cd write (iout,'(4e15.5)') sred_geom,
+cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
+cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
+cd & dabs(eello6(i,j,i+1,j1,jj,kk))
+ else if (wturn6.gt.0.0d0
+ & .and. (j.eq.i+4 .and. j1.eq.i+3)) then
+cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
+ eturn6=eturn6+eello_turn6(i,jj,kk)
+cd write (2,*) 'multibody_eello:eturn6',eturn6
+ endif
+ ENDIF
+1111 continue
+ else if (j1.eq.j) then
+C Contacts I-J and I-(J+1) occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
+ endif
+ enddo ! kk
+ do kk=1,num_conti
+ j1=jcont_hb(kk,i)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+c & ' jj=',jj,' kk=',kk
+ if (j1.eq.j+1) then
+C Contacts I-J and (I+1)-J occur simultaneously.
+C The system loses extra energy.
+c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
+ endif ! j1==j+1
+ enddo ! kk
+ enddo ! jj
+ enddo ! i
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function ehbcorr(i,j,k,l,jj,kk,coeffp,coeffm)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ double precision gx(3),gx1(3)
+ logical lprn
+ lprn=.false.
+ eij=facont_hb(jj,i)
+ ekl=facont_hb(kk,k)
+ ees0pij=ees0p(jj,i)
+ ees0pkl=ees0p(kk,k)
+ ees0mij=ees0m(jj,i)
+ ees0mkl=ees0m(kk,k)
+ ekont=eij*ekl
+ ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl)
+cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl)
+C Following 4 lines for diagnostics.
+cd ees0pkl=0.0D0
+cd ees0pij=1.0D0
+cd ees0mkl=0.0D0
+cd ees0mij=1.0D0
+c write (iout,*)'Contacts have occurred for peptide groups',i,j,
+c & ' and',k,l
+c write (iout,*)'Contacts have occurred for peptide groups',
+c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
+c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
+C Calculate the multi-body contribution to energy.
+ ecorr=ecorr+ekont*ees
+ if (calc_grad) then
+C Calculate multi-body contributions to the gradient.
+ do ll=1,3
+ ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i)
+ gradcorr(ll,i)=gradcorr(ll,i)+ghalf
+ & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb1(ll,jj,i))
+ gradcorr(ll,j)=gradcorr(ll,j)+ghalf
+ & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb2(ll,jj,i))
+ ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k)
+ gradcorr(ll,k)=gradcorr(ll,k)+ghalf
+ & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb1(ll,kk,k))
+ gradcorr(ll,l)=gradcorr(ll,l)+ghalf
+ & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb2(ll,kk,k))
+ enddo
+ do m=i+1,j-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+
+ & ees*ekl*gacont_hbr(ll,jj,i)-
+ & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
+ & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+
+ & ees*eij*gacont_hbr(ll,kk,k)-
+ & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
+ & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
+ enddo
+ enddo
+ endif
+ ehbcorr=ekont*ees
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine dipole(i,j,jj)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.FFIELD'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ dimension dipi(2,2),dipj(2,2),dipderi(2),dipderj(2),auxvec(2),
+ & auxmat(2,2)
+ iti1 = itortyp(itype(i+1))
+ if (j.lt.nres-1) then
+ itj1 = itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ do iii=1,2
+ dipi(iii,1)=Ub2(iii,i)
+ dipderi(iii)=Ub2der(iii,i)
+ dipi(iii,2)=b1(iii,iti1)
+ dipj(iii,1)=Ub2(iii,j)
+ dipderj(iii)=Ub2der(iii,j)
+ dipj(iii,2)=b1(iii,itj1)
+ enddo
+ kkk=0
+ do iii=1,2
+ call matvec2(a_chuj(1,1,jj,i),dipj(1,iii),auxvec(1))
+ do jjj=1,2
+ kkk=kkk+1
+ dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
+ enddo
+ enddo
+ if (.not.calc_grad) return
+ do kkk=1,5
+ do lll=1,3
+ mmm=0
+ do iii=1,2
+ call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),dipj(1,iii),
+ & auxvec(1))
+ do jjj=1,2
+ mmm=mmm+1
+ dipderx(lll,kkk,mmm,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
+ enddo
+ enddo
+ enddo
+ enddo
+ call transpose2(a_chuj(1,1,jj,i),auxmat(1,1))
+ call matvec2(auxmat(1,1),dipderi(1),auxvec(1))
+ do iii=1,2
+ dipderg(iii,jj,i)=scalar2(auxvec(1),dipj(1,iii))
+ enddo
+ call matvec2(a_chuj(1,1,jj,i),dipderj(1),auxvec(1))
+ do iii=1,2
+ dipderg(iii+2,jj,i)=scalar2(auxvec(1),dipi(1,iii))
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine calc_eello(i,j,k,l,jj,kk)
+C
+C This subroutine computes matrices and vectors needed to calculate
+C the fourth-, fifth-, and sixth-order local-electrostatic terms.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision aa1(2,2),aa2(2,2),aa1t(2,2),aa2t(2,2),
+ & aa1tder(2,2,3,5),aa2tder(2,2,3,5),auxmat(2,2)
+ logical lprn
+ common /kutas/ lprn
+cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l,
+cd & ' jj=',jj,' kk=',kk
+cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return
+ do iii=1,2
+ do jjj=1,2
+ aa1(iii,jjj)=a_chuj(iii,jjj,jj,i)
+ aa2(iii,jjj)=a_chuj(iii,jjj,kk,k)
+ enddo
+ enddo
+ call transpose2(aa1(1,1),aa1t(1,1))
+ call transpose2(aa2(1,1),aa2t(1,1))
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(a_chuj_der(1,1,lll,kkk,jj,i),
+ & aa1tder(1,1,lll,kkk))
+ call transpose2(a_chuj_der(1,1,lll,kkk,kk,k),
+ & aa2tder(1,1,lll,kkk))
+ enddo
+ enddo
+ if (l.eq.j+1) then
+C parallel orientation of the two CA-CA-CA frames.
+ if (i.gt.1) then
+ iti=itortyp(itype(i))
+ else
+ iti=ntortyp+1
+ endif
+ itk1=itortyp(itype(k+1))
+ itj=itortyp(itype(j))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+C A1 kernel(j+1) A2T
+cd do iii=1,2
+cd write (iout,'(3f10.5,5x,3f10.5)')
+cd & (EUg(iii,jjj,k),jjj=1,2),(EUg(iii,jjj,l),jjj=1,2)
+cd enddo
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.false.,EUg(1,1,l),EUgder(1,1,l),
+ & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0) THEN
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.false.,EUgC(1,1,l),EUgCder(1,1,l),
+ & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.false.,Ug2DtEUg(1,1,l),
+ & Ug2DtEUgder(1,1,1,l),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
+ & ADtEAderx(1,1,1,1,1,1))
+ lprn=.false.
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.false.,DtUg2EUg(1,1,l),
+ & DtUg2EUgder(1,1,1,l),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
+ & ADtEA1derx(1,1,1,1,1,1))
+ ENDIF
+C End 6-th order cumulants
+cd lprn=.false.
+cd if (lprn) then
+cd write (2,*) 'In calc_eello6'
+cd do iii=1,2
+cd write (2,*) 'iii=',iii
+cd do kkk=1,5
+cd write (2,*) 'kkk=',kkk
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
+cd enddo
+cd enddo
+cd enddo
+cd endif
+ call transpose2(EUgder(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & EAEAderx(1,1,lll,kkk,iii,1))
+ enddo
+ enddo
+ enddo
+C A1T kernel(i+1) A2
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUg(1,1,k),EUgder(1,1,k),
+ & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0) THEN
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUgC(1,1,k),EUgCder(1,1,k),
+ & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),2,.false.,Ug2DtEUg(1,1,k),
+ & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
+ & ADtEAderx(1,1,1,1,1,2))
+ call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,kk,k),2,.false.,DtUg2EUg(1,1,k),
+ & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
+ & ADtEA1derx(1,1,1,1,1,2))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,l),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEAderg(1,1,1,2))
+ call transpose2(EUg(1,1,l),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & EAEAderx(1,1,lll,kkk,iii,2))
+ enddo
+ enddo
+ enddo
+C AEAb1 and AEAb2
+C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
+C They are needed only when the fifth- or the sixth-order cumulants are
+C indluded.
+ IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
+ call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
+ call transpose2(AEAderg(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
+ call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
+ call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
+ call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
+ call transpose2(AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
+ call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
+ call transpose2(AEAderg(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
+ call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
+ call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
+ call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
+C Calculate the Cartesian derivatives of the vectors.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),
+ & AEAb1derx(1,lll,kkk,iii,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),
+ & AEAb2derx(1,lll,kkk,iii,1,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & AEAb1derx(1,lll,kkk,iii,2,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
+ & AEAb2derx(1,lll,kkk,iii,2,1))
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj),
+ & AEAb1derx(1,lll,kkk,iii,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,j),
+ & AEAb2derx(1,lll,kkk,iii,1,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ & AEAb1derx(1,lll,kkk,iii,2,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
+ & AEAb2derx(1,lll,kkk,iii,2,2))
+ enddo
+ enddo
+ enddo
+ ENDIF
+C End vectors
+ else
+C Antiparallel orientation of the two CA-CA-CA frames.
+ if (i.gt.1) then
+ iti=itortyp(itype(i))
+ else
+ iti=ntortyp+1
+ endif
+ itk1=itortyp(itype(k+1))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+C A2 kernel(j-1)T A1T
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.true.,EUg(1,1,j),EUgder(1,1,j),
+ & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
+ & j.eq.i+4 .and. l.eq.i+3)) THEN
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),1,.true.,EUgC(1,1,j),EUgCder(1,1,j),
+ & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
+ call kernel(aa2(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.true.,Ug2DtEUg(1,1,j),
+ & Ug2DtEUgder(1,1,1,j),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
+ & ADtEAderx(1,1,1,1,1,1))
+ call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
+ & aa2tder(1,1,1,1),2,.true.,DtUg2EUg(1,1,j),
+ & DtUg2EUgder(1,1,1,j),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
+ & ADtEA1derx(1,1,1,1,1,1))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & EAEAderx(1,1,lll,kkk,iii,1))
+ enddo
+ enddo
+ enddo
+C A2T kernel(i+1)T A1
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUg(1,1,k),EUgder(1,1,k),
+ & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
+C Following matrices are needed only for 6-th order cumulants
+ IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
+ & j.eq.i+4 .and. l.eq.i+3)) THEN
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUgC(1,1,k),EUgCder(1,1,k),
+ & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),2,.true.,Ug2DtEUg(1,1,k),
+ & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
+ & ADtEAderx(1,1,1,1,1,2))
+ call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
+ & a_chuj_der(1,1,1,1,jj,i),2,.true.,DtUg2EUg(1,1,k),
+ & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
+ & ADtEA1derx(1,1,1,1,1,2))
+ ENDIF
+C End 6-th order cumulants
+ call transpose2(EUgder(1,1,j),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,2,2))
+ call transpose2(EUg(1,1,j),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & EAEAderx(1,1,lll,kkk,iii,2))
+ enddo
+ enddo
+ enddo
+C AEAb1 and AEAb2
+C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
+C They are needed only when the fifth- or the sixth-order cumulants are
+C indluded.
+ IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
+ & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
+ call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
+ call transpose2(AEAderg(1,1,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
+ call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
+ call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
+ call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
+ call transpose2(AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
+ call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
+ call transpose2(AEAderg(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
+ call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
+ call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
+ call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
+C Calculate the Cartesian derivatives of the vectors.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,iti),
+ & AEAb1derx(1,lll,kkk,iii,1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i),
+ & AEAb2derx(1,lll,kkk,iii,1,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & AEAb1derx(1,lll,kkk,iii,2,1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
+ & AEAb2derx(1,lll,kkk,iii,2,1))
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),b1(1,itl),
+ & AEAb1derx(1,lll,kkk,iii,1,2))
+ call matvec2(auxmat(1,1),Ub2(1,l),
+ & AEAb2derx(1,lll,kkk,iii,1,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
+ & AEAb1derx(1,lll,kkk,iii,2,2))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
+ & AEAb2derx(1,lll,kkk,iii,2,2))
+ enddo
+ enddo
+ enddo
+ ENDIF
+C End vectors
+ endif
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine kernel(aa1,aa2t,aa1derx,aa2tderx,nderg,transp,
+ & KK,KKderg,AKA,AKAderg,AKAderx)
+ implicit none
+ integer nderg
+ logical transp
+ double precision aa1(2,2),aa2t(2,2),aa1derx(2,2,3,5),
+ & aa2tderx(2,2,3,5),KK(2,2),KKderg(2,2,nderg),AKA(2,2),
+ & AKAderg(2,2,nderg),AKAderx(2,2,3,5,2)
+ integer iii,kkk,lll
+ integer jjj,mmm
+ logical lprn
+ common /kutas/ lprn
+ call prodmat3(aa1(1,1),aa2t(1,1),KK(1,1),transp,AKA(1,1))
+ do iii=1,nderg
+ call prodmat3(aa1(1,1),aa2t(1,1),KKderg(1,1,iii),transp,
+ & AKAderg(1,1,iii))
+ enddo
+cd if (lprn) write (2,*) 'In kernel'
+ do kkk=1,5
+cd if (lprn) write (2,*) 'kkk=',kkk
+ do lll=1,3
+ call prodmat3(aa1derx(1,1,lll,kkk),aa2t(1,1),
+ & KK(1,1),transp,AKAderx(1,1,lll,kkk,1))
+cd if (lprn) then
+cd write (2,*) 'lll=',lll
+cd write (2,*) 'iii=1'
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & (AKAderx(jjj,mmm,lll,kkk,1),mmm=1,2)
+cd enddo
+cd endif
+ call prodmat3(aa1(1,1),aa2tderx(1,1,lll,kkk),
+ & KK(1,1),transp,AKAderx(1,1,lll,kkk,2))
+cd if (lprn) then
+cd write (2,*) 'lll=',lll
+cd write (2,*) 'iii=2'
+cd do jjj=1,2
+cd write (2,'(3(2f10.5),5x)')
+cd & (AKAderx(jjj,mmm,lll,kkk,2),mmm=1,2)
+cd enddo
+cd endif
+ enddo
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ double precision function eello4(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision pizda(2,2),ggg1(3),ggg2(3)
+cd if (i.ne.1 .or. j.ne.5 .or. k.ne.2 .or.l.ne.4) then
+cd eello4=0.0d0
+cd return
+cd endif
+cd print *,'eello4:',i,j,k,l,jj,kk
+cd write (2,*) 'i',i,' j',j,' k',k,' l',l
+cd call checkint4(i,j,k,l,jj,kk,eel4_num)
+cold eij=facont_hb(jj,i)
+cold ekl=facont_hb(kk,k)
+cold ekont=eij*ekl
+ eel4=-EAEA(1,1,1)-EAEA(2,2,1)
+ if (calc_grad) then
+cd eel41=-EAEA(1,1,2)-EAEA(2,2,2)
+ gcorr_loc(k-1)=gcorr_loc(k-1)
+ & -ekont*(EAEAderg(1,1,1,1)+EAEAderg(2,2,1,1))
+ if (l.eq.j+1) then
+ gcorr_loc(l-1)=gcorr_loc(l-1)
+ & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+ else
+ gcorr_loc(j-1)=gcorr_loc(j-1)
+ & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
+ endif
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=-EAEAderx(1,1,lll,kkk,iii,1)
+ & -EAEAderx(2,2,lll,kkk,iii,1)
+cd derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd gcorr_loc(l-1)=0.0d0
+cd gcorr_loc(j-1)=0.0d0
+cd gcorr_loc(k-1)=0.0d0
+cd eel4=1.0d0
+cd write (iout,*)'Contacts have occurred for peptide groups',
+cd & i,j,' fcont:',eij,' eij',' and ',k,l,
+cd & ' fcont ',ekl,' eel4=',eel4,' eel4_num',16*eel4_num
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i)
+ ggg1(ll)=eel4*g_contij(ll,1)
+ ggg2(ll)=eel4*g_contij(ll,2)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1)
+cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i)
+ gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k)
+ gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,gcorr_loc(iii)
+cd enddo
+ endif
+ eello4=ekont*eel4
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello4',ekont*eel4
+ return
+ end
+C---------------------------------------------------------------------------
+ double precision function eello5(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision pizda(2,2),auxmat(2,2),auxmat1(2,2),vv(2)
+ double precision ggg1(3),ggg2(3)
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C C
+C Parallel chains C
+C C
+C o o o o C
+C /l\ / \ \ / \ / \ / C
+C / \ / \ \ / \ / \ / C
+C j| o |l1 | o | o| o | | o |o C
+C \ |/k\| |/ \| / |/ \| |/ \| C
+C \i/ \ / \ / / \ / \ C
+C o k1 o C
+C (I) (II) (III) (IV) C
+C C
+C eello5_1 eello5_2 eello5_3 eello5_4 C
+C C
+C Antiparallel chains C
+C C
+C o o o o C
+C /j\ / \ \ / \ / \ / C
+C / \ / \ \ / \ / \ / C
+C j1| o |l | o | o| o | | o |o C
+C \ |/k\| |/ \| / |/ \| |/ \| C
+C \i/ \ / \ / / \ / \ C
+C o k1 o C
+C (I) (II) (III) (IV) C
+C C
+C eello5_1 eello5_2 eello5_3 eello5_4 C
+C C
+C o denotes a local interaction, vertical lines an electrostatic interaction. C
+C C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd if (i.ne.2 .or. j.ne.6 .or. k.ne.3 .or. l.ne.5) then
+cd eello5=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+ itk=itortyp(itype(k))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+ eello5_1=0.0d0
+ eello5_2=0.0d0
+ eello5_3=0.0d0
+ eello5_4=0.0d0
+cd call checkint5(i,j,k,l,jj,kk,eel5_1_num,eel5_2_num,
+cd & eel5_3_num,eel5_4_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=facont_hb(jj,i)
+cd ekl=facont_hb(kk,k)
+cd ekont=eij*ekl
+cd write (iout,*)'Contacts have occurred for peptide groups',
+cd & i,j,' fcont:',eij,' eij',' and ',k,l
+cd goto 1111
+C Contribution from the graph I.
+cd write (2,*) 'AEA ',AEA(1,1,1),AEA(2,1,1),AEA(1,2,1),AEA(2,2,1)
+cd write (2,*) 'AEAb2',AEAb2(1,1,1),AEAb2(2,1,1)
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,i)))
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(AEA(1,1,1),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2(1,1,1),Ub2der(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ call matmat2(AEAderg(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ if (l.eq.j+1) then
+ if (l.lt.nres-1) g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ else
+ if (j.lt.nres-1) g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
+ endif
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,1),Ub2(1,k))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
+ enddo
+ enddo
+ enddo
+c goto 1112
+ endif
+c1111 continue
+C Contribution from graph II
+ call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,k))
+ call matmat2(auxmat(1,1),AEAderg(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ if (l.eq.j+1) then
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
+ else
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
+ endif
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,k))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+cd1111 continue
+ if (l.eq.j+1) then
+cd goto 1110
+C Parallel orientation
+C Contribution from graph III
+ call transpose2(EUg(1,1,l),auxmat(1,1))
+ call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,j)))
+ call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
+ call transpose2(EUgder(1,1,l),auxmat1(1,1))
+ call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,l))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+C Contribution from graph IV
+cd1110 continue
+ call transpose2(EE(1,1,itl),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,l))
+ enddo
+ enddo
+ enddo
+ endif
+ else
+C Antiparallel orientation
+C Contribution from graph III
+c goto 1110
+ call transpose2(EUg(1,1,j),auxmat(1,1))
+ call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(l-1)=g_corr5_loc(l-1)
+ & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2der(1,l)))
+ call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
+ call transpose2(EUgder(1,1,j),auxmat1(1,1))
+ call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
+ & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,j))
+ & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
+ enddo
+ enddo
+ enddo
+cd goto 1112
+ endif
+C Contribution from graph IV
+1110 continue
+ call transpose2(EE(1,1,itj),auxmat(1,1))
+ call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j))
+ if (calc_grad) then
+C Explicit gradient in virtual-dihedral angles.
+ g_corr5_loc(j-1)=g_corr5_loc(j-1)
+ & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,j))
+ call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ g_corr5_loc(k-1)=g_corr5_loc(k-1)
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j)))
+C Cartesian gradient
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
+ & -0.5d0*scalar2(vv(1),Ctobr(1,j))
+ enddo
+ enddo
+ enddo
+ endif
+ endif
+1112 continue
+ eel5=eello5_1+eello5_2+eello5_3+eello5_4
+cd if (i.eq.2 .and. j.eq.8 .and. k.eq.3 .and. l.eq.7) then
+cd write (2,*) 'ijkl',i,j,k,l
+cd write (2,*) 'eello5_1',eello5_1,' eello5_2',eello5_2,
+cd & ' eello5_3',eello5_3,' eello5_4',eello5_4
+cd endif
+cd write(iout,*) 'eello5_1',eello5_1,' eel5_1_num',16*eel5_1_num
+cd write(iout,*) 'eello5_2',eello5_2,' eel5_2_num',16*eel5_2_num
+cd write(iout,*) 'eello5_3',eello5_3,' eel5_3_num',16*eel5_3_num
+cd write(iout,*) 'eello5_4',eello5_4,' eel5_4_num',16*eel5_4_num
+ if (calc_grad) then
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont
+ do ll=1,3
+ ggg1(ll)=eel5*g_contij(ll,1)
+ ggg2(ll)=eel5*g_contij(ll,2)
+cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1)
+cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i)
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k)
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
+ enddo
+ enddo
+c1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr5_loc(iii)
+cd enddo
+ endif
+ eello5=ekont*eel5
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello5',ekont*eel5
+ return
+ end
+c--------------------------------------------------------------------------
+ double precision function eello6(i,j,k,l,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision ggg1(3),ggg2(3)
+cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
+cd eello6=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+ eello6_1=0.0d0
+ eello6_2=0.0d0
+ eello6_3=0.0d0
+ eello6_4=0.0d0
+ eello6_5=0.0d0
+ eello6_6=0.0d0
+cd call checkint6(i,j,k,l,jj,kk,eel6_1_num,eel6_2_num,
+cd & eel6_3_num,eel6_4_num,eel6_5_num,eel6_6_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=facont_hb(jj,i)
+cd ekl=facont_hb(kk,k)
+cd ekont=eij*ekl
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+ if (l.eq.j+1) then
+ eello6_1=eello6_graph1(i,j,k,l,1,.false.)
+ eello6_2=eello6_graph1(j,i,l,k,2,.false.)
+ eello6_3=eello6_graph2(i,j,k,l,jj,kk,.false.)
+ eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
+ eello6_5=eello6_graph4(j,i,l,k,jj,kk,2,.false.)
+ eello6_6=eello6_graph3(i,j,k,l,jj,kk,.false.)
+ else
+ eello6_1=eello6_graph1(i,j,k,l,1,.false.)
+ eello6_2=eello6_graph1(l,k,j,i,2,.true.)
+ eello6_3=eello6_graph2(i,l,k,j,jj,kk,.true.)
+ eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
+ if (wturn6.eq.0.0d0 .or. j.ne.i+4) then
+ eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
+ else
+ eello6_5=0.0d0
+ endif
+ eello6_6=eello6_graph3(i,l,k,j,jj,kk,.true.)
+ endif
+C If turn contributions are considered, they will be handled separately.
+ eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6
+cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num
+cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num
+cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num
+cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num
+cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num
+cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num
+cd goto 1112
+ if (calc_grad) then
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+ ggg1(ll)=eel6*g_contij(ll,1)
+ ggg2(ll)=eel6*g_contij(ll,2)
+cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1)
+ gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1)
+ ghalf=0.5d0*ggg2(ll)
+cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k)
+cd ghalf=0.0d0
+ gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2)
+ gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i)
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k)
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr6_loc(iii)
+cd enddo
+ endif
+ eello6=ekont*eel6
+cd write (2,*) 'ekont',ekont
+cd write (iout,*) 'eello6',ekont*eel6
+ return
+ end
+c--------------------------------------------------------------------------
+ double precision function eello6_graph1(i,j,k,l,imat,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vv(2),vv1(2),pizda(2,2),auxmat(2,2),pizda1(2,2)
+ logical swap
+ logical lprn
+ common /kutas/ lprn
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Parallel Antiparallel
+C
+C o o
+C /l\ /j\
+C / \ / \
+C /| o | | o |\
+C \ j|/k\| / \ |/k\|l /
+C \ / \ / \ / \ /
+C o o o o
+C i i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+ itk=itortyp(itype(k))
+ s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
+ s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
+ s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
+ call transpose2(EUgC(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
+ vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
+ vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
+ s5=scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
+ eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
+ if (.not. calc_grad) return
+ if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1)
+ & -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i))
+ & -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,2,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2der(1,i))
+ & +scalar2(vv(1),Dtobr2der(1,i)))
+ call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
+ vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
+ if (l.eq.j+1) then
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)
+ & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
+ & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)
+ & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
+ & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
+ & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
+ endif
+ call transpose2(EUgCder(1,1,k),auxmat(1,1))
+ call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ if (k.gt.1) g_corr6_loc(k-1)=g_corr6_loc(k-1)
+ & +ekont*(-0.5d0*(-scalar2(AEAb2(1,1,imat),Ug2Db1tder(1,k))
+ & +scalar2(AEAb2(1,1,imat),CUgb2der(1,k))
+ & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))))
+ do iii=1,2
+ if (swap) then
+ ind=3-iii
+ else
+ ind=iii
+ endif
+ do kkk=1,5
+ do lll=1,3
+ s1= scalar2(AEAb1derx(1,lll,kkk,iii,2,imat),CUgb2(1,i))
+ s2=-scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),Ug2Db1t(1,k))
+ s3= scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),CUgb2(1,k))
+ call transpose2(EUgC(1,1,k),auxmat(1,1))
+ call matmat2(AEAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
+ & pizda1(1,1))
+ vv1(1)=pizda1(1,1)-pizda1(2,2)
+ vv1(2)=pizda1(1,2)+pizda1(2,1)
+ s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
+ vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
+ & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
+ vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
+ & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
+ s5=scalar2(vv(1),Dtobr2(1,i))
+ derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph2(i,j,k,l,jj,kk,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ logical swap
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
+ & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ logical lprn
+ common /kutas/ lprn
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Parallel Antiparallel
+C
+C o o
+C \ /l\ /j\ /
+C \ / \ / \ /
+C o| o | | o |o
+C \ j|/k\| \ |/k\|l
+C \ / \ \ / \
+C o o
+C i i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
+C AL 7/4/01 s1 would occur in the sixth-order moment,
+C but not in a cluster cumulant
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dip(1,kk,k)
+#endif
+ call matvec2(ADtEA1(1,1,1),Ub2(1,k),auxvec(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matvec2(ADtEA(1,1,2),Ub2(1,l),auxvec1(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec1(1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(ADtEA1(1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 'eello6_graph2:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph2=-(s1+s2+s3+s4)
+#else
+ eello6_graph2=-(s2+s3+s4)
+#endif
+c eello6_graph2=-s3
+ if (.not. calc_grad) return
+C Derivatives in gamma(i-1)
+ if (i.gt.1) then
+#ifdef MOMENT
+ s1=dipderg(1,jj,i)*dip(1,kk,k)
+#endif
+ s2=-0.5d0*scalar2(Ub2der(1,i),auxvec(1))
+ call matvec2(ADtEAderg(1,1,1,2),Ub2(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ s4=-0.25d0*scalar2(vv(1),Dtobr2der(1,i))
+#ifdef MOMENT
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
+#endif
+c g_corr6_loc(i-1)=g_corr6_loc(i-1)-s3
+ endif
+C Derivatives in gamma(k-1)
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dipderg(1,kk,k)
+#endif
+ call matvec2(ADtEA1(1,1,1),Ub2der(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ call matvec2(ADtEAderg(1,1,2,2),Ub2(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(ADtEA1(1,1,1),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
+#endif
+c g_corr6_loc(k-1)=g_corr6_loc(k-1)-s3
+C Derivatives in gamma(j-1) or gamma(l-1)
+ if (j.gt.1) then
+#ifdef MOMENT
+ s1=dipderg(3,jj,i)*dip(1,kk,k)
+#endif
+ call matvec2(ADtEA1derg(1,1,1,1),Ub2(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2der(1,j),auxvec1(1))
+ call matmat2(ADtEA1derg(1,1,1,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ if (swap) then
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
+ endif
+#endif
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s3+s4)
+c g_corr6_loc(j-1)=g_corr6_loc(j-1)-s3
+ endif
+C Derivatives in gamma(l-1) or gamma(j-1)
+ if (l.gt.1) then
+#ifdef MOMENT
+ s1=dip(1,jj,i)*dipderg(3,kk,k)
+#endif
+ call matvec2(ADtEA1derg(1,1,2,1),Ub2(1,k),auxvec2(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
+ call matvec2(ADtEA(1,1,2),Ub2der(1,l),auxvec2(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
+ call matmat2(ADtEA1derg(1,1,2,1),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+#ifdef MOMENT
+ if (swap) then
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
+ else
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
+ endif
+#endif
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s3+s4)
+c g_corr6_loc(l-1)=g_corr6_loc(l-1)-s3
+ endif
+C Cartesian derivatives.
+ if (lprn) then
+ write (2,*) 'In eello6_graph2'
+ do iii=1,2
+ write (2,*) 'iii=',iii
+ do kkk=1,5
+ write (2,*) 'kkk=',kkk
+ do jjj=1,2
+ write (2,'(3(2f10.5),5x)')
+ & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
+ enddo
+ enddo
+ enddo
+ endif
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ s1=dipderx(lll,kkk,1,jj,i)*dip(1,kk,k)
+ else
+ s1=dip(1,jj,i)*dipderx(lll,kkk,1,kk,k)
+ endif
+#endif
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,1),Ub2(1,k),
+ & auxvec(1))
+ s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matvec2(ADtEAderx(1,1,lll,kkk,iii,2),Ub2(1,l),
+ & auxvec(1))
+ s3=-0.5d0*scalar2(Ub2(1,j),auxvec(1))
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(ADtEA1derx(1,1,lll,kkk,iii,1),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(1,2)+pizda(2,1)
+ s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (swap) then
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph3(i,j,k,l,jj,kk,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
+ logical swap
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Parallel Antiparallel
+C
+C o o
+C /l\ / \ /j\
+C / \ / \ / \
+C /| o |o o| o |\
+C j|/k\| / |/k\|l /
+C / \ / / \ /
+C / o / o
+C i i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C 4/7/01 AL Component s1 was removed, because it pertains to the respective
+C energy moment and not to the cluster cumulant.
+ iti=itortyp(itype(i))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ itk=itortyp(itype(k))
+ itk1=itortyp(itype(k+1))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+#ifdef MOMENT
+ s1=dip(4,jj,i)*dip(4,kk,k)
+#endif
+ call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph3=-(s1+s2+s3+s4)
+#else
+ eello6_graph3=-(s2+s3+s4)
+#endif
+c eello6_graph3=-s4
+ if (.not. calc_grad) return
+C Derivatives in gamma(k-1)
+ call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
+C Derivatives in gamma(l-1)
+ call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
+C Cartesian derivatives.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ s1=dipderx(lll,kkk,4,jj,i)*dip(4,kk,k)
+ else
+ s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
+ endif
+#endif
+ call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ & auxvec(1))
+ s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ & auxvec(1))
+ s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)+pizda(2,2)
+ vv(2)=pizda(2,1)-pizda(1,2)
+ s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (swap) then
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+c derx(lll,kkk,iii)=derx(lll,kkk,iii)-s4
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.FFIELD'
+ double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
+ & auxvec1(2),auxmat1(2,2)
+ logical swap
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C Parallel Antiparallel
+C
+C o o
+C /l\ / \ /j\
+C / \ / \ / \
+C /| o |o o| o |\
+C \ j|/k\| \ |/k\|l
+C \ / \ \ / \
+C o \ o \
+C i i
+C
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+C
+C 4/7/01 AL Component s1 was removed, because it pertains to the respective
+C energy moment and not to the cluster cumulant.
+cd write (2,*) 'eello_graph4: wturn6',wturn6
+ iti=itortyp(itype(i))
+ itj=itortyp(itype(j))
+ if (j.lt.nres-1) then
+ itj1=itortyp(itype(j+1))
+ else
+ itj1=ntortyp+1
+ endif
+ itk=itortyp(itype(k))
+ if (k.lt.nres-1) then
+ itk1=itortyp(itype(k+1))
+ else
+ itk1=ntortyp+1
+ endif
+ itl=itortyp(itype(l))
+ if (l.lt.nres-1) then
+ itl1=itortyp(itype(l+1))
+ else
+ itl1=ntortyp+1
+ endif
+cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
+cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
+cd & ' itl',itl,' itl1',itl1
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dip(3,kk,k)
+ else
+ s1=dip(2,jj,j)*dip(2,kk,l)
+ endif
+#endif
+ call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ call transpose2(EUg(1,1,k),auxmat(1,1))
+ call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+cd write (2,*) 'eello6_graph4:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+#ifdef MOMENT
+ eello6_graph4=-(s1+s2+s3+s4)
+#else
+ eello6_graph4=-(s2+s3+s4)
+#endif
+ if (.not. calc_grad) return
+C Derivatives in gamma(i-1)
+ if (i.gt.1) then
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dipderg(2,jj,i)*dip(3,kk,k)
+ else
+ s1=dipderg(4,jj,j)*dip(2,kk,l)
+ endif
+#endif
+ s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+cd write (2,*) 'turn6 derivatives'
+#ifdef MOMENT
+ gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s2+s3+s4)
+#endif
+ else
+#ifdef MOMENT
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
+#endif
+ endif
+ endif
+C Derivatives in gamma(k-1)
+#ifdef MOMENT
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dipderg(2,kk,k)
+ else
+ s1=dip(2,jj,j)*dipderg(4,kk,l)
+ endif
+#endif
+ call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ else
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ endif
+ call transpose2(EUgder(1,1,k),auxmat1(1,1))
+ call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+#ifdef MOMENT
+ gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s2+s3+s4)
+#endif
+ else
+#ifdef MOMENT
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
+#else
+ g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
+#endif
+ endif
+C Derivatives in gamma(j-1) or gamma(l-1)
+ if (l.eq.j+1 .and. l.gt.1) then
+ call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
+ else if (j.gt.1) then
+ call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+ gel_loc_turn6(j-1)=gel_loc_turn6(j-1)-ekont*(s2+s4)
+ else
+ g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s4)
+ endif
+ endif
+C Cartesian derivatives.
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ if (iii.eq.1) then
+ if (imat.eq.1) then
+ s1=dipderx(lll,kkk,3,jj,i)*dip(3,kk,k)
+ else
+ s1=dipderx(lll,kkk,2,jj,j)*dip(2,kk,l)
+ endif
+ else
+ if (imat.eq.1) then
+ s1=dip(3,jj,i)*dipderx(lll,kkk,3,kk,k)
+ else
+ s1=dip(2,jj,j)*dipderx(lll,kkk,2,kk,l)
+ endif
+ endif
+#endif
+ call matvec2(AECAderx(1,1,lll,kkk,iii,imat),Ub2(1,k),
+ & auxvec(1))
+ s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
+ if (j.eq.l+1) then
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
+ & b1(1,itj1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
+ else
+ call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
+ & b1(1,itl1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
+ endif
+ call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
+ & pizda(1,1))
+ vv(1)=pizda(1,1)-pizda(2,2)
+ vv(2)=pizda(2,1)+pizda(1,2)
+ s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
+ if (swap) then
+ if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
+#ifdef MOMENT
+ derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
+ & -(s1+s2+s4)
+#else
+ derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
+ & -(s2+s4)
+#endif
+ derx_turn(lll,kkk,iii)=derx_turn(lll,kkk,iii)-s3
+ else
+#ifdef MOMENT
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s2+s4)
+#endif
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ endif
+ else
+#ifdef MOMENT
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
+#else
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
+#endif
+ if (l.eq.j+1) then
+ derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
+ else
+ derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
+ endif
+ endif
+ enddo
+ enddo
+ enddo
+ return
+ end
+c----------------------------------------------------------------------------
+ double precision function eello_turn6(i,jj,kk)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ double precision vtemp1(2),vtemp2(2),vtemp3(2),vtemp4(2),
+ & atemp(2,2),auxmat(2,2),achuj_temp(2,2),gtemp(2,2),gvec(2),
+ & ggg1(3),ggg2(3)
+ double precision vtemp1d(2),vtemp2d(2),vtemp3d(2),vtemp4d(2),
+ & atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2)
+C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to
+C the respective energy moment and not to the cluster cumulant.
+ eello_turn6=0.0d0
+ j=i+4
+ k=i+1
+ l=i+3
+ iti=itortyp(itype(i))
+ itk=itortyp(itype(k))
+ itk1=itortyp(itype(k+1))
+ itl=itortyp(itype(l))
+ itj=itortyp(itype(j))
+cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
+cd write (2,*) 'i',i,' k',k,' j',j,' l',l
+cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
+cd eello6=0.0d0
+cd return
+cd endif
+cd write (iout,*)
+cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
+cd & ' and',k,l
+cd call checkint_turn6(i,jj,kk,eel_turn6_num)
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+ derx_turn(lll,kkk,iii)=0.0d0
+ enddo
+ enddo
+ enddo
+cd eij=1.0d0
+cd ekl=1.0d0
+cd ekont=1.0d0
+ eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
+cd eello6_5=0.0d0
+cd write (2,*) 'eello6_5',eello6_5
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmat(1,1))
+ call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
+ ss1=scalar2(Ub2(1,i+2),b1(1,itl))
+ s1 = (auxmat(1,1)+auxmat(2,2))*ss1
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
+ s2 = scalar2(b1(1,itk),vtemp1(1))
+#ifdef MOMENT
+ call transpose2(AEA(1,1,2),atemp(1,1))
+ call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
+ call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
+ s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#endif
+ call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
+ call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
+ s12 = scalar2(Ub2(1,i+2),vtemp3(1))
+#ifdef MOMENT
+ call transpose2(a_chuj(1,1,kk,i+1),achuj_temp(1,1))
+ call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
+ call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
+ call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
+ ss13 = scalar2(b1(1,itk),vtemp4(1))
+ s13 = (gtemp(1,1)+gtemp(2,2))*ss13
+#endif
+c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
+c s1=0.0d0
+c s2=0.0d0
+c s8=0.0d0
+c s12=0.0d0
+c s13=0.0d0
+ eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13)
+ if (calc_grad) then
+C Derivatives in gamma(i+2)
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmatd(1,1))
+ call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+ call transpose2(AEAderg(1,1,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#endif
+ call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+ gel_loc_turn6(i)=gel_loc_turn6(i)-0.5d0*ekont*(s1d+s8d+s12d)
+C Derivatives in gamma(i+3)
+#ifdef MOMENT
+ call transpose2(AEA(1,1,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
+#endif
+ call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
+ s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
+#endif
+ s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
+#ifdef MOMENT
+ call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
+ s13d = (gtempd(1,1)+gtempd(2,2))*ss13
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
+ & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
+#else
+ gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
+ & -0.5d0*ekont*(s2d+s12d)
+#endif
+C Derivatives in gamma(i+4)
+ call matmat2(EUgder(1,1,i+3),AEA(1,1,2),auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+#ifdef MOMENT
+ call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1))
+ s13d = (gtempd(1,1)+gtempd(2,2))*ss13
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+C s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d+s13d)
+#else
+ gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d)
+#endif
+C Derivatives in gamma(i+5)
+#ifdef MOMENT
+ call transpose2(AEAderg(1,1,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call transpose2(AEA(1,1,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
+#endif
+ call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+#ifdef MOMENT
+ call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
+ ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
+#endif
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
+ & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
+#else
+ gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
+ & -0.5d0*ekont*(s2d+s12d)
+#endif
+C Cartesian derivatives
+ do iii=1,2
+ do kkk=1,5
+ do lll=1,3
+#ifdef MOMENT
+ call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1))
+ call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
+ s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
+#endif
+ call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
+ & vtemp1d(1))
+ s2d = scalar2(b1(1,itk),vtemp1d(1))
+#ifdef MOMENT
+ call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
+ call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
+ s8d = -(atempd(1,1)+atempd(2,2))*
+ & scalar2(cc(1,1,itl),vtemp2(1))
+#endif
+ call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
+ & auxmatd(1,1))
+ call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
+ s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
+c s1d=0.0d0
+c s2d=0.0d0
+c s8d=0.0d0
+c s12d=0.0d0
+c s13d=0.0d0
+#ifdef MOMENT
+ derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
+ & - 0.5d0*(s1d+s2d)
+#else
+ derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
+ & - 0.5d0*s2d
+#endif
+#ifdef MOMENT
+ derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
+ & - 0.5d0*(s8d+s12d)
+#else
+ derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
+ & - 0.5d0*s12d
+#endif
+ enddo
+ enddo
+ enddo
+#ifdef MOMENT
+ do kkk=1,5
+ do lll=1,3
+ call transpose2(a_chuj_der(1,1,lll,kkk,kk,i+1),
+ & achuj_tempd(1,1))
+ call matmat2(achuj_tempd(1,1),EUg(1,1,i+2),gtempd(1,1))
+ call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
+ s13d=(gtempd(1,1)+gtempd(2,2))*ss13
+ derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
+ call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
+ & vtemp4d(1))
+ ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
+ derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
+ enddo
+ enddo
+#endif
+cd write(iout,*) 'eel6_turn6',eel_turn6,' eel_turn6_num',
+cd & 16*eel_turn6_num
+cd goto 1112
+ if (j.lt.nres-1) then
+ j1=j+1
+ j2=j-1
+ else
+ j1=j-1
+ j2=j-2
+ endif
+ if (l.lt.nres-1) then
+ l1=l+1
+ l2=l-1
+ else
+ l1=l-1
+ l2=l-2
+ endif
+ do ll=1,3
+ ggg1(ll)=eel_turn6*g_contij(ll,1)
+ ggg2(ll)=eel_turn6*g_contij(ll,2)
+ ghalf=0.5d0*ggg1(ll)
+cd ghalf=0.0d0
+ gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf
+ & +ekont*derx_turn(ll,2,1)
+ gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1)
+ gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf
+ & +ekont*derx_turn(ll,4,1)
+ gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1)
+ ghalf=0.5d0*ggg2(ll)
+cd ghalf=0.0d0
+ gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf
+ & +ekont*derx_turn(ll,2,2)
+ gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2)
+ gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf
+ & +ekont*derx_turn(ll,4,2)
+ gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2)
+ enddo
+cd goto 1112
+ do m=i+1,j-1
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
+ enddo
+ enddo
+ do m=k+1,l-1
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
+ enddo
+ enddo
+1112 continue
+ do m=i+2,j2
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
+ enddo
+ enddo
+ do m=k+2,l2
+ do ll=1,3
+ gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
+ enddo
+ enddo
+cd do iii=1,nres-3
+cd write (2,*) iii,g_corr6_loc(iii)
+cd enddo
+ endif
+ eello_turn6=ekont*eel_turn6
+cd write (2,*) 'ekont',ekont
+cd write (2,*) 'eel_turn6',ekont*eel_turn6
+ return
+ end
+crc-------------------------------------------------
+ SUBROUTINE MATVEC2(A1,V1,V2)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ DIMENSION A1(2,2),V1(2),V2(2)
+c DO 1 I=1,2
+c VI=0.0
+c DO 3 K=1,2
+c 3 VI=VI+A1(I,K)*V1(K)
+c Vaux(I)=VI
+c 1 CONTINUE
+
+ vaux1=a1(1,1)*v1(1)+a1(1,2)*v1(2)
+ vaux2=a1(2,1)*v1(1)+a1(2,2)*v1(2)
+
+ v2(1)=vaux1
+ v2(2)=vaux2
+ END
+C---------------------------------------
+ SUBROUTINE MATMAT2(A1,A2,A3)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ DIMENSION A1(2,2),A2(2,2),A3(2,2)
+c DIMENSION AI3(2,2)
+c DO J=1,2
+c A3IJ=0.0
+c DO K=1,2
+c A3IJ=A3IJ+A1(I,K)*A2(K,J)
+c enddo
+c A3(I,J)=A3IJ
+c enddo
+c enddo
+
+ ai3_11=a1(1,1)*a2(1,1)+a1(1,2)*a2(2,1)
+ ai3_12=a1(1,1)*a2(1,2)+a1(1,2)*a2(2,2)
+ ai3_21=a1(2,1)*a2(1,1)+a1(2,2)*a2(2,1)
+ ai3_22=a1(2,1)*a2(1,2)+a1(2,2)*a2(2,2)
+
+ A3(1,1)=AI3_11
+ A3(2,1)=AI3_21
+ A3(1,2)=AI3_12
+ A3(2,2)=AI3_22
+ END
+
+c-------------------------------------------------------------------------
+ double precision function scalar2(u,v)
+ implicit none
+ double precision u(2),v(2)
+ double precision sc
+ integer i
+ scalar2=u(1)*v(1)+u(2)*v(2)
+ return
+ end
+
+C-----------------------------------------------------------------------------
+
+ subroutine transpose2(a,at)
+ implicit none
+ double precision a(2,2),at(2,2)
+ at(1,1)=a(1,1)
+ at(1,2)=a(2,1)
+ at(2,1)=a(1,2)
+ at(2,2)=a(2,2)
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine transpose(n,a,at)
+ implicit none
+ integer n,i,j
+ double precision a(n,n),at(n,n)
+ do i=1,n
+ do j=1,n
+ at(j,i)=a(i,j)
+ enddo
+ enddo
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine prodmat3(a1,a2,kk,transp,prod)
+ implicit none
+ integer i,j
+ double precision a1(2,2),a2(2,2),a2t(2,2),kk(2,2),prod(2,2)
+ logical transp
+crc double precision auxmat(2,2),prod_(2,2)
+
+ if (transp) then
+crc call transpose2(kk(1,1),auxmat(1,1))
+crc call matmat2(a1(1,1),auxmat(1,1),auxmat(1,1))
+crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
+
+ prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,1)
+ & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,1)
+ prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,2)
+ & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,2)
+ prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,1)
+ & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,1)
+ prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,2)
+ & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,2)
+
+ else
+crc call matmat2(a1(1,1),kk(1,1),auxmat(1,1))
+crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
+
+ prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,1)
+ & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,1)
+ prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,2)
+ & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,2)
+ prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,1)
+ & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,1)
+ prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,2)
+ & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,2)
+
+ endif
+c call transpose2(a2(1,1),a2t(1,1))
+
+crc print *,transp
+crc print *,((prod_(i,j),i=1,2),j=1,2)
+crc print *,((prod(i,j),i=1,2),j=1,2)
+
+ return
+ end
+C-----------------------------------------------------------------------------
+ double precision function scalar(u,v)
+ implicit none
+ double precision u(3),v(3)
+ double precision sc
+ integer i
+ sc=0.0d0
+ do i=1,3
+ sc=sc+u(i)*v(i)
+ enddo
+ scalar=sc
+ return
+ end
+
--- /dev/null
+ subroutine fitsq(rms,x,y,nn,t,b,non_conv)
+ implicit real*8 (a-h,o-z)
+ include 'COMMON.IOUNITS'
+c x and y are the vectors of coordinates (dimensioned (3,n)) of the two
+c structures to be superimposed. nn is 3*n, where n is the number of
+c points. t and b are respectively the translation vector and the
+c rotation matrix that transforms the second set of coordinates to the
+c frame of the first set.
+c eta = machine-specific variable
+
+ dimension x(3*nn),y(3*nn),t(3)
+ dimension b(3,3),q(3,3),r(3,3),v(3),xav(3),yav(3),e(3),c(3,3)
+ logical non_conv
+ eta = z00100000
+c small=25.0*rmdcon(3)
+c small=25.0*eta
+c small=25.0*10.e-10
+c the following is a very lenient value for 'small'
+ small = 0.0001D0
+ non_conv=.false.
+ fn=nn
+ do 10 i=1,3
+ xav(i)=0.0D0
+ yav(i)=0.0D0
+ do 10 j=1,3
+ 10 b(j,i)=0.0D0
+ nc=0
+c
+ do 30 n=1,nn
+ do 20 i=1,3
+crc write(iout,*)'x = ',x(nc+i),' y = ',y(nc+i)
+ xav(i)=xav(i)+x(nc+i)/fn
+ 20 yav(i)=yav(i)+y(nc+i)/fn
+ 30 nc=nc+3
+c
+ do i=1,3
+ t(i)=yav(i)-xav(i)
+ enddo
+
+ rms=0.0d0
+ do n=1,nn
+ do i=1,3
+ rms=rms+(y(3*(n-1)+i)-x(3*(n-1)+i)-t(i))**2
+ enddo
+ enddo
+ rms=dabs(rms/fn)
+
+c write(iout,*)'xav = ',(xav(j),j=1,3)
+c write(iout,*)'yav = ',(yav(j),j=1,3)
+c write(iout,*)'t = ',(t(j),j=1,3)
+c write(iout,*)'rms=',rms
+ if (rms.lt.small) return
+
+
+ nc=0
+ rms=0.0D0
+ do 50 n=1,nn
+ do 40 i=1,3
+ rms=rms+((x(nc+i)-xav(i))**2+(y(nc+i)-yav(i))**2)/fn
+ do 40 j=1,3
+ b(j,i)=b(j,i)+(x(nc+i)-xav(i))*(y(nc+j)-yav(j))/fn
+ 40 c(j,i)=b(j,i)
+ 50 nc=nc+3
+ call sivade(b,q,r,d,non_conv)
+ sn3=dsign(1.0d0,d)
+ do 120 i=1,3
+ do 120 j=1,3
+ 120 b(j,i)=-q(j,1)*r(i,1)-q(j,2)*r(i,2)-sn3*q(j,3)*r(i,3)
+ call mvvad(b,xav,yav,t)
+ do 130 i=1,3
+ do 130 j=1,3
+ rms=rms+2.0*c(j,i)*b(j,i)
+ 130 b(j,i)=-b(j,i)
+ if (dabs(rms).gt.small) go to 140
+* write (6,301)
+ return
+ 140 if (rms.gt.0.0d0) go to 150
+c write (iout,303) rms
+ rms=0.0d0
+* stop
+c 150 write (iout,302) dsqrt(rms)
+ 150 continue
+ return
+ 301 format (5x,'rms deviation negligible')
+ 302 format (5x,'rms deviation ',f14.6)
+ 303 format (//,5x,'negative ms deviation - ',f14.6)
+ end
+ subroutine sivade(x,q,r,dt,non_conv)
+ implicit real*8(a-h,o-z)
+c computes q,e and r such that q(t)xr = diag(e)
+ dimension x(3,3),q(3,3),r(3,3),e(3)
+ dimension h(3,3),p(3,3),u(3,3),d(3)
+ logical non_conv
+ eta = z00100000
+ nit = 0
+ small=25.0*10.e-10
+c small=25.0*eta
+c small=2.0*rmdcon(3)
+ xnrm=0.0d0
+ do 20 i=1,3
+ do 10 j=1,3
+ xnrm=xnrm+x(j,i)*x(j,i)
+ u(j,i)=0.0d0
+ r(j,i)=0.0d0
+ 10 h(j,i)=0.0d0
+ u(i,i)=1.0
+ 20 r(i,i)=1.0
+ xnrm=dsqrt(xnrm)
+ do 110 n=1,2
+ xmax=0.0d0
+ do 30 j=n,3
+ 30 if (dabs(x(j,n)).gt.xmax) xmax=dabs(x(j,n))
+ a=0.0d0
+ do 40 j=n,3
+ h(j,n)=x(j,n)/xmax
+ 40 a=a+h(j,n)*h(j,n)
+ a=dsqrt(a)
+ den=a*(a+dabs(h(n,n)))
+ d(n)=1.0/den
+ h(n,n)=h(n,n)+dsign(a,h(n,n))
+ do 70 i=n,3
+ s=0.0d0
+ do 50 j=n,3
+ 50 s=s+h(j,n)*x(j,i)
+ s=d(n)*s
+ do 60 j=n,3
+ 60 x(j,i)=x(j,i)-s*h(j,n)
+ 70 continue
+ if (n.gt.1) go to 110
+ xmax=dmax1(dabs(x(1,2)),dabs(x(1,3)))
+ h(2,3)=x(1,2)/xmax
+ h(3,3)=x(1,3)/xmax
+ a=dsqrt(h(2,3)*h(2,3)+h(3,3)*h(3,3))
+ den=a*(a+dabs(h(2,3)))
+ d(3)=1.0/den
+ h(2,3)=h(2,3)+sign(a,h(2,3))
+ do 100 i=1,3
+ s=0.0d0
+ do 80 j=2,3
+ 80 s=s+h(j,3)*x(i,j)
+ s=d(3)*s
+ do 90 j=2,3
+ 90 x(i,j)=x(i,j)-s*h(j,3)
+ 100 continue
+ 110 continue
+ do 130 i=1,3
+ do 120 j=1,3
+ 120 p(j,i)=-d(1)*h(j,1)*h(i,1)
+ 130 p(i,i)=1.0+p(i,i)
+ do 140 i=2,3
+ do 140 j=2,3
+ u(j,i)=u(j,i)-d(2)*h(j,2)*h(i,2)
+ 140 r(j,i)=r(j,i)-d(3)*h(j,3)*h(i,3)
+ call mmmul(p,u,q)
+ 150 np=1
+ nq=1
+ nit=nit+1
+ if (nit.gt.10000) then
+ print '(a)','!!!! Over 10000 iterations in SIVADE!!!!!'
+ non_conv=.true.
+ return
+ endif
+ if (dabs(x(2,3)).gt.small*(dabs(x(2,2))+abs(x(3,3)))) go to 160
+ x(2,3)=0.0d0
+ nq=nq+1
+ 160 if (dabs(x(1,2)).gt.small*(dabs(x(1,1))+dabs(x(2,2)))) go to 180
+ x(1,2)=0.0d0
+ if (x(2,3).ne.0.0d0) go to 170
+ nq=nq+1
+ go to 180
+ 170 np=np+1
+ 180 if (nq.eq.3) go to 310
+ npq=4-np-nq
+ if (np.gt.npq) go to 230
+ n0=0
+ do 220 n=np,npq
+ nn=n+np-1
+ if (dabs(x(nn,nn)).gt.small*xnrm) go to 220
+ x(nn,nn)=0.0d0
+ if (x(nn,nn+1).eq.0.0d0) go to 220
+ n0=n0+1
+ go to (190,210,220),nn
+ 190 do 200 j=2,3
+ 200 call givns(x,q,1,j)
+ go to 220
+ 210 call givns(x,q,2,3)
+ 220 continue
+ if (n0.ne.0) go to 150
+ 230 nn=3-nq
+ a=x(nn,nn)*x(nn,nn)
+ if (nn.gt.1) a=a+x(nn-1,nn)*x(nn-1,nn)
+ b=x(nn+1,nn+1)*x(nn+1,nn+1)+x(nn,nn+1)*x(nn,nn+1)
+ c=x(nn,nn)*x(nn,nn+1)
+ dd=0.5*(a-b)
+ xn2=c*c
+ rt=b-xn2/(dd+sign(dsqrt(dd*dd+xn2),dd))
+ y=x(np,np)*x(np,np)-rt
+ z=x(np,np)*x(np,np+1)
+ do 300 n=np,nn
+ if (dabs(y).lt.dabs(z)) go to 240
+ t=z/y
+ c=1.0/dsqrt(1.0d0+t*t)
+ s=c*t
+ go to 250
+ 240 t=y/z
+ s=1.0/dsqrt(1.0d0+t*t)
+ c=s*t
+ 250 do 260 j=1,3
+ v=x(j,n)
+ w=x(j,n+1)
+ x(j,n)=c*v+s*w
+ x(j,n+1)=-s*v+c*w
+ a=r(j,n)
+ b=r(j,n+1)
+ r(j,n)=c*a+s*b
+ 260 r(j,n+1)=-s*a+c*b
+ y=x(n,n)
+ z=x(n+1,n)
+ if (dabs(y).lt.dabs(z)) go to 270
+ t=z/y
+ c=1.0/dsqrt(1.0+t*t)
+ s=c*t
+ go to 280
+ 270 t=y/z
+ s=1.0/dsqrt(1.0+t*t)
+ c=s*t
+ 280 do 290 j=1,3
+ v=x(n,j)
+ w=x(n+1,j)
+ a=q(j,n)
+ b=q(j,n+1)
+ x(n,j)=c*v+s*w
+ x(n+1,j)=-s*v+c*w
+ q(j,n)=c*a+s*b
+ 290 q(j,n+1)=-s*a+c*b
+ if (n.ge.nn) go to 300
+ y=x(n,n+1)
+ z=x(n,n+2)
+ 300 continue
+ go to 150
+ 310 do 320 i=1,3
+ 320 e(i)=x(i,i)
+ nit=0
+ 330 n0=0
+ nit=nit+1
+ if (nit.gt.10000) then
+ print '(a)','!!!! Over 10000 iterations in SIVADE!!!!!'
+ non_conv=.true.
+ return
+ endif
+ do 360 i=1,3
+ if (e(i).ge.0.0d0) go to 350
+ e(i)=-e(i)
+ do 340 j=1,3
+ 340 q(j,i)=-q(j,i)
+ 350 if (i.eq.1) go to 360
+ if (dabs(e(i)).lt.dabs(e(i-1))) go to 360
+ call switch(i,1,q,r,e)
+ n0=n0+1
+ 360 continue
+ if (n0.ne.0) go to 330
+ if (dabs(e(3)).gt.small*xnrm) go to 370
+ e(3)=0.0d0
+ if (dabs(e(2)).gt.small*xnrm) go to 370
+ e(2)=0.0d0
+ 370 dt=det(q(1,1),q(1,2),q(1,3))*det(r(1,1),r(1,2),r(1,3))
+* write (1,501) (e(i),i=1,3)
+ return
+ 501 format (/,5x,'singular values - ',3e15.5)
+ end
+ subroutine givns(a,b,m,n)
+ implicit real*8 (a-h,o-z)
+ dimension a(3,3),b(3,3)
+ if (dabs(a(m,n)).lt.dabs(a(n,n))) go to 10
+ t=a(n,n)/a(m,n)
+ s=1.0/dsqrt(1.0+t*t)
+ c=s*t
+ go to 20
+ 10 t=a(m,n)/a(n,n)
+ c=1.0/dsqrt(1.0+t*t)
+ s=c*t
+ 20 do 30 j=1,3
+ v=a(m,j)
+ w=a(n,j)
+ x=b(j,m)
+ y=b(j,n)
+ a(m,j)=c*v-s*w
+ a(n,j)=s*v+c*w
+ b(j,m)=c*x-s*y
+ 30 b(j,n)=s*x+c*y
+ return
+ end
+ subroutine switch(n,m,u,v,d)
+ implicit real*8 (a-h,o-z)
+ dimension u(3,3),v(3,3),d(3)
+ do 10 i=1,3
+ tem=u(i,n)
+ u(i,n)=u(i,n-1)
+ u(i,n-1)=tem
+ if (m.eq.0) go to 10
+ tem=v(i,n)
+ v(i,n)=v(i,n-1)
+ v(i,n-1)=tem
+ 10 continue
+ tem=d(n)
+ d(n)=d(n-1)
+ d(n-1)=tem
+ return
+ end
+ subroutine mvvad(b,xav,yav,t)
+ implicit real*8 (a-h,o-z)
+ dimension b(3,3),xav(3),yav(3),t(3)
+c dimension a(3,3),b(3),c(3),d(3)
+c do 10 j=1,3
+c d(j)=c(j)
+c do 10 i=1,3
+c 10 d(j)=d(j)+a(j,i)*b(i)
+ do 10 j=1,3
+ t(j)=yav(j)
+ do 10 i=1,3
+ 10 t(j)=t(j)+b(j,i)*xav(i)
+ return
+ end
+ double precision function det (a,b,c)
+ implicit real*8 (a-h,o-z)
+ dimension a(3),b(3),c(3)
+ det=a(1)*(b(2)*c(3)-b(3)*c(2))+a(2)*(b(3)*c(1)-b(1)*c(3))
+ 1 +a(3)*(b(1)*c(2)-b(2)*c(1))
+ return
+ end
+ subroutine mmmul(a,b,c)
+ implicit real*8 (a-h,o-z)
+ dimension a(3,3),b(3,3),c(3,3)
+ do 10 i=1,3
+ do 10 j=1,3
+ c(i,j)=0.0d0
+ do 10 k=1,3
+ 10 c(i,j)=c(i,j)+a(i,k)*b(k,j)
+ return
+ end
+ subroutine matvec(uvec,tmat,pvec,nback)
+ implicit real*8 (a-h,o-z)
+ real*8 tmat(3,3),uvec(3,nback), pvec(3,nback)
+c
+ do 2 j=1,nback
+ do 1 i=1,3
+ uvec(i,j) = 0.0d0
+ do 1 k=1,3
+ 1 uvec(i,j)=uvec(i,j)+tmat(i,k)*pvec(k,j)
+ 2 continue
+ return
+ end
--- /dev/null
+ subroutine pdbout(ii,temp,efree,etot,entropy,rmsdev)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.HEADER'
+ include 'COMMON.SBRIDGE'
+ character*50 tytul
+ dimension ica(maxres)
+ write(ipdb,'("REMARK CONF",i8," TEMPERATURE",f7.1," RMS",0pf7.2)')
+ & ii,temp,rmsdev
+ write (ipdb,'("REMARK DIMENSIONLESS FREE ENERGY",1pe15.5)')
+ & efree
+ write (ipdb,'("REMARK ENERGY",1pe15.5," ENTROPY",1pe15.5)')
+ & etot,entropy
+ iatom=0
+ do i=nnt,nct
+ ires=i-nnt+1
+ iatom=iatom+1
+ ica(i)=iatom
+ iti=itype(i)
+ write (ipdb,10) iatom,restyp(iti),ires,(c(j,i),j=1,3)
+ if (iti.ne.10) then
+ iatom=iatom+1
+ write (ipdb,20) iatom,restyp(iti),ires,(c(j,nres+i),j=1,3)
+ endif
+ enddo
+ write (ipdb,'(a)') 'TER'
+ do i=nnt,nct-1
+ if (itype(i).eq.10) then
+ write (ipdb,30) ica(i),ica(i+1)
+ else
+ write (ipdb,30) ica(i),ica(i+1),ica(i)+1
+ endif
+ enddo
+ if (itype(nct).ne.10) then
+ write (ipdb,30) ica(nct),ica(nct)+1
+ endif
+ do i=1,nss
+ write (ipdb,30) ica(ihpb(i))+1,ica(jhpb(i))+1
+ enddo
+ write (ipdb,'(a)') "END"
+ 10 FORMAT ('ATOM',I7,' CA ',A3,I6,4X,3F8.3)
+ 20 FORMAT ('ATOM',I7,' CB ',A3,I6,4X,3F8.3)
+ 30 FORMAT ('CONECT',8I5)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine MOL2out(etot,tytul)
+C Prints the Cartesian coordinates of the alpha-carbons in the Tripos mol2
+C format.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.HEADER'
+ include 'COMMON.SBRIDGE'
+ character*32 tytul,fd
+ character*3 liczba
+ character*6 res_num,pom,ucase
+#ifdef AIX
+ call fdate_(fd)
+#else
+ call fdate(fd)
+#endif
+ write (imol2,'(a)') '#'
+ write (imol2,'(a)')
+ & '# Creating user name: unres'
+ write (imol2,'(2a)') '# Creation time: ',
+ & fd
+ write (imol2,'(/a)') '\@<TRIPOS>MOLECULE'
+ write (imol2,'(a)') tytul
+ write (imol2,'(5i5)') nct-nnt+1,nct-nnt+nss+1,nct-nnt+nss+1,0,0
+ write (imol2,'(a)') 'SMALL'
+ write (imol2,'(a)') 'USER_CHARGES'
+ write (imol2,'(a)') '\@<TRIPOS>ATOM'
+ do i=nnt,nct
+ write (liczba,*) i
+ pom=ucase(restyp(itype(i)))
+ res_num = pom(:3)//liczba(2:)
+ write (imol2,10) i,(c(j,i),j=1,3),i,res_num,0.0
+ enddo
+ write (imol2,'(a)') '\@<TRIPOS>BOND'
+ do i=nnt,nct-1
+ write (imol2,'(i5,2i6,i2)') i-nnt+1,i-nnt+1,i-nnt+2,1
+ enddo
+ do i=1,nss
+ write (imol2,'(i5,2i6,i2)') nct-nnt+i,ihpb(i),jhpb(i),1
+ enddo
+ write (imol2,'(a)') '\@<TRIPOS>SUBSTRUCTURE'
+ do i=nnt,nct
+ write (liczba,*) i
+ pom = ucase(restyp(itype(i)))
+ res_num = pom(:3)//liczba(2:)
+ write (imol2,30) i-nnt+1,res_num,i-nnt+1,0
+ enddo
+ 10 FORMAT (I7,' CA ',3F10.4,' C.3',I8,1X,A,F11.4,' ****')
+ 30 FORMAT (I7,1x,A,I14,' RESIDUE',I13,' **** ****')
+ return
+ end
+c------------------------------------------------------------------------
+ subroutine intout
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.GEO'
+ write (iout,'(/a)') 'Geometry of the virtual chain.'
+ write (iout,'(7a)') ' Res ',' Dpep',' Theta',
+ & ' Phi',' Dsc',' Alpha',' Omega'
+ do i=1,nres
+ iti=itype(i)
+ write (iout,'(a3,i4,6f10.3)') restyp(iti),i,vbld(i+1),
+ & rad2deg*theta(i),
+ & rad2deg*phi(i),vbld(nres+i),rad2deg*alph(i),rad2deg*omeg(i)
+ enddo
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine briefout(it,ener)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.GEO'
+ include 'COMMON.SBRIDGE'
+ print '(a,i5)',intname,igeom
+#if defined(AIX) || defined(PGI)
+ open (igeom,file=intname,position='append')
+#else
+ open (igeom,file=intname,access='append')
+#endif
+ IF (NSS.LE.9) THEN
+ WRITE (igeom,180) IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)
+ ELSE
+ WRITE (igeom,180) IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,9)
+ WRITE (igeom,190) (IHPB(I),JHPB(I),I=10,NSS)
+ ENDIF
+c IF (nvar.gt.nphi) WRITE (igeom,200) (RAD2DEG*THETA(I),I=3,NRES)
+ WRITE (igeom,200) (RAD2DEG*THETA(I),I=3,NRES)
+ WRITE (igeom,200) (RAD2DEG*PHI(I),I=4,NRES)
+c if (nvar.gt.nphi+ntheta) then
+ write (igeom,200) (rad2deg*alph(i),i=2,nres-1)
+ write (igeom,200) (rad2deg*omeg(i),i=2,nres-1)
+c endif
+ close(igeom)
+ 180 format (I5,F12.3,I2,9(1X,2I3))
+ 190 format (3X,11(1X,2I3))
+ 200 format (8F10.4)
+ return
+ end
--- /dev/null
+ double precision function gnmr1(y,ymin,ymax)
+ implicit none
+ double precision y,ymin,ymax
+ double precision wykl /4.0d0/
+ if (y.lt.ymin) then
+ gnmr1=(ymin-y)**wykl/wykl
+ else if (y.gt.ymax) then
+ gnmr1=(y-ymax)**wykl/wykl
+ else
+ gnmr1=0.0d0
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function gnmr1prim(y,ymin,ymax)
+ implicit none
+ double precision y,ymin,ymax
+ double precision wykl /4.0d0/
+ if (y.lt.ymin) then
+ gnmr1prim=-(ymin-y)**(wykl-1)
+ else if (y.gt.ymax) then
+ gnmr1prim=(y-ymax)**(wykl-1)
+ else
+ gnmr1prim=0.0d0
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ double precision function harmonic(y,ymax)
+ implicit none
+ double precision y,ymax
+ double precision wykl /2.0d0/
+ harmonic=(y-ymax)**wykl
+ return
+ end
+c-------------------------------------------------------------------------------
+ double precision function harmonicprim(y,ymax)
+ double precision y,ymin,ymax
+ double precision wykl /2.0d0/
+ harmonicprim=(y-ymax)*wykl
+ return
+ end
+c---------------------------------------------------------------------------------
--- /dev/null
+ INTEGER FUNCTION ICANT(I,J)
+ IF (I.GE.J) THEN
+ ICANT=(I*(I-1))/2+J
+ ELSE
+ ICANT=(J*(J-1))/2+I
+ ENDIF
+ RETURN
+ END
+
--- /dev/null
+ integer i,j,k,l
+ double precision erij,rij,xj,yj,zj,dxi,dyi,dzi,dxj,dyj,dzj,
+ & chi1,chi2,chi12,chip1,chip2,chip12,alf1,alf2,alf12,om1,om2,om12,
+ & om1om2,chiom1,chiom2,chiom12,chipom1,chipom2,chipom12,eps1,
+ & faceps1,faceps1_inv,eps1_om12,facsig,sigsq,sigsq_om1,sigsq_om2,
+ & sigsq_om12,facp,facp_inv,facp1,eps2rt,eps2rt_om1,eps2rt_om2,
+ & eps2rt_om12,eps3rt,eom1,eom2,eom12,evdwij,eps2der,eps3der,sigder,
+ & dsci_inv,dscj_inv,gg
+ common /calc/ erij(3),rij,xj,yj,zj,dxi,dyi,dzi,dxj,dyj,dzj,
+ & chi1,chi2,chi12,chip1,chip2,chip12,alf1,alf2,alf12,om1,om2,om12,
+ & om1om2,chiom1,chiom2,chiom12,chipom1,chipom2,chipom12,eps1,
+ & faceps1,faceps1_inv,eps1_om12,facsig,sigsq,sigsq_om1,sigsq_om2,
+ & sigsq_om12,facp,facp_inv,facp1,eps2rt,eps2rt_om1,eps2rt_om2,
+ & eps2rt_om12,eps3rt,eom1,eom2,eom12,evdwij,eps2der,eps3der,sigder,
+ & dsci_inv,dscj_inv,gg(3),i,j
--- /dev/null
+C Change 12/1/95 - common block CONTACTS1 included.
+ integer ncont,ncont_ref,icont,icont_ref,num_cont,jcont
+ double precision facont,gacont
+ common /contacts/ ncont,ncont_ref,icont(2,maxcont),
+ & icont_ref(2,maxcont)
+ common /contacts1/ facont(maxconts,maxres),
+ & gacont(3,maxconts,maxres),
+ & num_cont(maxres),jcont(maxconts,maxres)
+C 12/26/95 - H-bonding contacts
+ common /contacts_hb/
+ & gacontp_hb1(3,maxconts,maxres),gacontp_hb2(3,maxconts,maxres),
+ & gacontp_hb3(3,maxconts,maxres),
+ & gacontm_hb1(3,maxconts,maxres),gacontm_hb2(3,maxconts,maxres),
+ & gacontm_hb3(3,maxconts,maxres),
+ & gacont_hbr(3,maxconts,maxres),
+ & grij_hb_cont(3,maxconts,maxres),
+ & facont_hb(maxconts,maxres),ees0p(maxconts,maxres),
+ & ees0m(maxconts,maxres),d_cont(maxconts,maxres),
+ & num_cont_hb(maxres),jcont_hb(maxconts,maxres)
+C 9/23/99 Added improper rotation matrices and matrices of dipole-dipole
+C interactions
+C Interactions of pseudo-dipoles generated by loc-el interactions.
+ double precision dip,dipderg,dipderx
+ common /dipint/ dip(4,maxconts,maxres),dipderg(4,maxconts,maxres),
+ & dipderx(3,5,4,maxconts,maxres)
+C 10/30/99 Added other pre-computed vectors and matrices needed
+C to calculate three - six-order el-loc correlation terms
+ double precision Ug,Ugder,Ug2,Ug2der,obrot,obrot2,obrot_der,
+ & obrot2_der,Ub2,Ub2der,mu,muder,EUg,EUgder,CUg,CUgder,
+ & DUg,DUgder,DtUg2,DtUg2der,Ctobr,Ctobrder,Dtobr2,Dtobr2der
+ common /rotat/ Ug(2,2,maxres),Ugder(2,2,maxres),Ug2(2,2,maxres),
+ & Ug2der(2,2,maxres),obrot(2,maxres),obrot2(2,maxres),
+ & obrot_der(2,maxres),obrot2_der(2,maxres)
+C This common block contains vectors and matrices dependent on a single
+C amino-acid residue.
+ common /precomp1/ Ub2(2,maxres),Ub2der(2,maxres),mu(2,maxres),
+ & EUg(2,2,maxres),EUgder(2,2,maxres),CUg(2,2,maxres),
+ & CUgder(2,2,maxres),DUg(2,2,maxres),Dugder(2,2,maxres),
+ & DtUg2(2,2,maxres),DtUg2der(2,2,maxres),Ctobr(2,maxres),
+ & Ctobrder(2,maxres),Dtobr2(2,maxres),Dtobr2der(2,maxres)
+C This common block contains vectors and matrices dependent on two
+C consecutive amino-acid residues.
+ double precision Ug2Db1t,Ug2Db1tder,CUgb2,CUgb2der,EUgC,
+ & EUgCder,EUgD,EUgDder,DtUg2EUg,DtUg2EUgder
+ common /precomp2/ Ug2Db1t(2,maxres),Ug2Db1tder(2,maxres),
+ & CUgb2(2,maxres),CUgb2der(2,maxres),EUgC(2,2,maxres),
+ & EUgCder(2,2,maxres),EUgD(2,2,maxres),EUgDder(2,2,maxres),
+ & DtUg2EUg(2,2,maxres),DtUg2EUgder(2,2,2,maxres),
+ & Ug2DtEUg(2,2,maxres),Ug2DtEUgder(2,2,2,maxres)
+ double precision costab,sintab,costab2,sintab2
+ common /rotat_old/ costab(maxres),sintab(maxres),
+ & costab2(maxres),sintab2(maxres),muder(2,maxres)
+C This common block contains dipole-interaction matrices and their
+C Cartesian derivatives.
+ double precision a_chuj,a_chuj_der
+ common /dipmat/ a_chuj(2,2,maxconts,maxres),
+ & a_chuj_der(2,2,3,5,maxconts,maxres)
+ double precision AEA,AEAderg,AEAderx,AECA,AECAderg,AECAderx,
+ & ADtEA,ADtEAderg,ADtEAderx,AEAb1,AEAb1derg,AEAb1derx,
+ & AEAb2,AEAb2derg,AEAb2derx
+ common /diploc/ AEA(2,2,2),AEAderg(2,2,2),AEAderx(2,2,3,5,2,2),
+ & EAEA(2,2,2), EAEAderg(2,2,2,2), EAEAderx(2,2,3,5,2,2),
+ & AECA(2,2,2),AECAderg(2,2,2),AECAderx(2,2,3,5,2,2),
+ & ADtEA(2,2,2),ADtEAderg(2,2,2,2),ADtEAderx(2,2,3,5,2,2),
+ & ADtEA1(2,2,2),ADtEA1derg(2,2,2,2),ADtEA1derx(2,2,3,5,2,2),
+ & AEAb1(2,2,2),AEAb1derg(2,2,2),AEAb1derx(2,3,5,2,2,2),
+ & AEAb2(2,2,2),AEAb2derg(2,2,2,2),AEAb2derx(2,3,5,2,2,2),
+ & g_contij(3,2),ekont
--- /dev/null
+ double precision sig_comp,chi_comp,chip_comp,sc_cutoff
+ common /contpar/ sig_comp(ntyp,ntyp),chi_comp(ntyp,ntyp),
+ & chip_comp(ntyp,ntyp),sc_cutoff(ntyp,ntyp)
--- /dev/null
+ double precision dcdv,dxdv,dxds,gradx,gradc,gvdwc,gelc,gvdwpp,
+ & gradx_scp,gvdwc_scp,ghpbx,ghpbc,gloc,gvdwx,gradcorr,gradxorr,
+ & gradcorr5,gradcorr6,gel_loc,gcorr3_turn,gcorr4_turn,gcorr6_turn,
+ & gel_loc_loc,gel_loc_turn3,gel_loc_turn4,gel_loc_turn6,gcorr_loc,
+ & g_corr5_loc,g_corr6_loc,gradb,gradbx,gsccorc,gsccorx,gsccor_loc,
+ & gscloc,gsclocx
+ integer nfl,icg
+ logical calc_grad
+ common /derivat/ dcdv(6,maxdim),dxdv(6,maxdim),dxds(6,maxres),
+ & gradx(3,maxres,2),gradc(3,maxres,2),gvdwx(3,maxres),
+ & gvdwc(3,maxres),gelc(3,maxres),gvdwpp(3,maxres),
+ & gradx_scp(3,maxres),
+ & gvdwc_scp(3,maxres),ghpbx(3,maxres),ghpbc(3,maxres),
+ & gloc(maxvar,2),gradcorr(3,maxres),gradxorr(3,maxres),
+ & gradcorr5(3,maxres),gradcorr6(3,maxres),
+ & gel_loc(3,maxres),gcorr3_turn(3,maxres),gcorr4_turn(3,maxres),
+ & gcorr6_turn(3,maxres),gradb(3,maxres),gradbx(3,maxres),
+ & gel_loc_loc(maxvar),gel_loc_turn3(maxvar),gel_loc_turn4(maxvar),
+ & gel_loc_turn6(maxvar),gcorr_loc(maxvar),
+ & g_corr5_loc(maxvar),g_corr6_loc(maxvar),gsccorc(3,maxres),
+ & gsccorx(3,maxres),gsccor_loc(maxres),
+ & gscloc(3,maxres),gsclocx(3,maxres),nfl,icg,calc_grad
+ double precision derx,derx_turn
+ common /deriv_loc/ derx(3,5,2),derx_turn(3,5,2)
+ double precision dXX_C1tab(3,maxres),dYY_C1tab(3,maxres),
+ & dZZ_C1tab(3,maxres),dXX_Ctab(3,maxres),dYY_Ctab(3,maxres),
+ & dZZ_Ctab(3,maxres),dXX_XYZtab(3,maxres),dYY_XYZtab(3,maxres),
+ & dZZ_XYZtab(3,maxres)
+ common /deriv_scloc/ dXX_C1tab,dYY_C1tab,dZZ_C1tab,dXX_Ctab,
+ & dYY_Ctab,dZZ_Ctab,dXX_XYZtab,dYY_XYZtab,dZZ_XYZtab
--- /dev/null
+C-----------------------------------------------------------------------
+C The following COMMON block selects the type of the force field used in
+C calculations and defines weights of various energy terms.
+C 12/1/95 wcorr added
+C-----------------------------------------------------------------------
+ double precision wsc,wscp,welec,wstrain,wtor,wtor_d,wang,wscloc,
+ & wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,
+ & wturn6,wvdwpp,wbond,weights,scal14,cutoff_corr,delt_corr,
+ & r0_corr
+ integer ipot,n_ene_comp
+ common /ffield/ wsc,wscp,welec,wstrain,wtor,wtor_d,wang,wscloc,
+ & wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,
+ & wturn6,wvdwpp,wbond,weights(max_ene),
+ & scal14,cutoff_corr,delt_corr,r0_corr,ipot,n_ene_comp
+ common /potentials/ potname(6)
+ character*3 potname
+C-----------------------------------------------------------------------
+C wlong,welec,wtor,wang,wscloc are the weight of the energy terms
+C corresponding to side-chain, electrostatic, torsional, valence-angle,
+C and local side-chain terms.
+C
+C IPOT determines which SC...SC interaction potential will be used:
+C 1 - LJ: 2n-n Lennard-Jones
+C 2 - LJK: 2n-n Kihara type (shifted Lennard-Jones)
+C 3 - BP; Berne-Pechukas (angular dependence)
+C 4 - GB; Gay-Berne (angular dependence)
+C 5 - GBV; Gay-Berne-Vorobjev; angularly-dependent Kihara potential
+C 6 - MM; Momo's physics-based potentials
+C------------------------------------------------------------------------
--- /dev/null
+ integer nbfrag,bfrag,nhfrag,hfrag,bvar_frag,hvar_frag,nhpb0,
+ & nh310frag,h310frag
+ COMMON /c_frag/ nbfrag,bfrag(4,maxres/3),nhfrag,hfrag(2,maxres/3),
+ & nh310frag,h310frag(2,maxres/2)
+ COMMON /frag/ bvar_frag(mxio,6),hvar_frag(mxio,3)
--- /dev/null
+ double precision pi,dwapi,pipol,pi3,dwapi3,deg2rad,rad2deg,angmin
+ common /geo/ pi,dwapi,pipol,pi3,dwapi3,deg2rad,rad2deg,angmin
--- /dev/null
+ character*80 titel
+ common /header/ titel
--- /dev/null
+ double precision aa,bb,augm,aad,bad,app,bpp,ael6,ael3,
+ & chis,alphasur,sigmap1,sigmap2,alphiso,rborn,sigiso1,sigiso2,
+ & sig0head,epshead,wquad,dhead,dtail,wqdip,alphapol,wstate,
+ & epsintab,eps_out
+
+ integer nnt,nct,nint_gr,istart,iend,itype,itel,itypro,ielstart,
+ & ielend,nscp_gr,iscpstart,iscpend,iatsc_s,iatsc_e,iatel_s,
+ & iatel_e,iatscp_s,iatscp_e,ispp,iscp,nstate,icharge,expon,expon2
+ common /interact/aa(ntyp,ntyp),bb(ntyp,ntyp),augm(ntyp,ntyp),
+ & chis(ntyp,ntyp),alphasur(4,ntyp,ntyp),sigmap1(ntyp,ntyp),
+ & sigmap2(ntyp,ntyp),alphiso(4,ntyp,ntyp),alphapol(ntyp,ntyp),
+ & rborn(ntyp,ntyp),sigiso1(ntyp,ntyp),sigiso2(ntyp,ntyp),
+ & epshead(ntyp,ntyp),wquad(ntyp,ntyp),dhead(2,2,ntyp,ntyp),
+ & dtail(2,ntyp,ntyp),wqdip(2,ntyp,ntyp),epsintab(ntyp,ntyp),
+ & eps_out,wstate(4,ntyp,ntyp),sig0head(ntyp,ntyp),
+ & aad(ntyp,2),bad(ntyp,2),app(2,2),bpp(2,2),ael6(2,2),ael3(2,2),
+ & expon,expon2,nnt,nct,nint_gr(maxres),istart(maxres,maxint_gr),
+ & iend(maxres,maxint_gr),itype(maxres),itel(maxres),itypro,
+ & ielstart(maxres),ielend(maxres),nscp_gr(maxres),
+ & iscpstart(maxres,maxint_gr),iscpend(maxres,maxint_gr),
+ & iatsc_s,iatsc_e,iatel_s,iatel_e,iatscp_s,iatscp_e,ispp,iscp,
+ & nstate(ntyp,ntyp)
+C 12/1/95 Array EPS included in the COMMON block.
+ double precision eps,sigma,sigmaii,rs0,chi,chip,chip0,alp,sigma0,
+ & sigii,rr0,r0,r0e,r0d,rpp,epp,elpp6,elpp3,eps_scp,rscp,
+ & chipp,eps_orig
+ common /body/eps(ntyp,ntyp),sigma(0:ntyp,0:ntyp),
+ & sigmaii(ntyp,ntyp),
+ & rs0(ntyp,ntyp),chi(ntyp,ntyp),chipp(ntyp,ntyp),chip(ntyp),
+ & chip0(ntyp),alp(ntyp),
+ & sigma0(ntyp),sigii(ntyp),rr0(ntyp),r0(ntyp,ntyp),r0e(ntyp,ntyp),
+ & r0d(ntyp,2),rpp(2,2),epp(2,2),elpp6(2,2),elpp3(2,2),
+ & eps_scp(20,2),rscp(20,2),eps_orig(ntyp,ntyp),icharge(ntyp)
+c 12/5/03 modified 09/18/03 Bond stretching parameters.
+ double precision vbldp0,vbldsc0,akp,aksc,abond0
+ integer nbondterm
+ common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
+ & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),nbondterm(ntyp)
--- /dev/null
+ double precision a0thet,athet,bthet,polthet,gthet,theta0,sig0,
+ & sigc0,dsc,dsc_inv,bsc,censc,gaussc,dsc0,vbl,vblinv,vblinv2,
+ & vbl_cis,vbl0,vbld_inv
+ integer nlob,loc_start,loc_end,ithet_start,ithet_end,
+ & iphi_start,iphi_end,itau_start,itau_end
+C Parameters of the virtual-bond-angle probability distribution
+ common /thetas/ a0thet(ntyp),athet(2,ntyp),bthet(2,ntyp),
+ & polthet(0:3,ntyp),gthet(3,ntyp),theta0(ntyp),sig0(ntyp),
+ & sigc0(ntyp)
+C Parameters of ab initio-derived potential of virtual-bond-angle bending
+ integer nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,ndouble,
+ & ithetyp(ntyp1),nntheterm
+ double precision aa0thet(maxthetyp1,maxthetyp1,maxthetyp1),
+ & aathet(maxtheterm,maxthetyp1,maxthetyp1,maxthetyp1),
+ & bbthet(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,maxthetyp1),
+ & ccthet(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,maxthetyp1),
+ & ddthet(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,maxthetyp1),
+ & eethet(maxsingle,maxtheterm2,maxthetyp1,maxthetyp1,maxthetyp1),
+ & ffthet(maxdouble,maxdouble,maxtheterm3,maxthetyp1,maxthetyp1,
+ & maxthetyp1),
+ & ggthet(maxdouble,maxdouble,maxtheterm3,maxthetyp1,maxthetyp1,
+ & maxthetyp1)
+ common /theta_abinitio/aa0thet,aathet,bbthet,ccthet,ddthet,eethet,
+ & ffthet,
+ & ggthet,ithetyp,nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,
+ & ndouble,nntheterm
+C Parameters of the side-chain probability distribution
+ common /sclocal/ dsc(ntyp1),dsc_inv(ntyp1),bsc(maxlob,ntyp),
+ & censc(3,maxlob,ntyp),gaussc(3,3,maxlob,ntyp),dsc0(ntyp1),
+ & nlob(ntyp1)
+C Virtual-bond lenghts
+ common /peptbond/ vbl,vblinv,vblinv2,vbl_cis,vbl0
+ common /indices/ loc_start,loc_end,ithet_start,ithet_end,
+ & iphi_start,iphi_end,itau_start,itau_end
+C Inverses of the actual virtual bond lengths
+ common /invlen/ vbld_inv(maxres2)
--- /dev/null
+ double precision tolf,rtolf
+ integer maxfun,maxmin
+ common /minimm/ tolf,rtolf,maxfun,maxmin
--- /dev/null
+ character*3 restyp
+ character*1 onelet
+ common /names/ restyp(ntyp+1),onelet(ntyp+1)
+ character*10 ename,wname
+ integer nprint_ene,print_order
+ common /namterm/ ename(max_ene),wname(max_ene),nprint_ene,
+ & print_order(max_ene)
--- /dev/null
+ double precision ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,dhpb,
+ & dhpb1,forcon,weidis
+ integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end,
+ & ibecarb
+ common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
+ & nfree,iss(maxss)
+ common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
+ & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
+ common /restraints/ weidis
+ common /links_split/ link_start,link_end
--- /dev/null
+cc Parameters of the SCCOR term
+ double precision v1sccor,v2sccor,vlor1sccor,
+ & vlor2sccor,vlor3sccor,gloc_sc,
+ & dcostau,dsintau,dtauangle,dcosomicron,
+ & domicron,v0sccor
+ integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
+ common /sccor/ v1sccor(maxterm_sccor,3,20,20),
+ & v2sccor(maxterm_sccor,3,20,20),
+ & v0sccor(ntyp,ntyp),
+ & vlor1sccor(maxterm_sccor,20,20),
+ & vlor2sccor(maxterm_sccor,20,20),
+ & vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
+ & dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
+ & dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
+ & domicron(3,3,3,maxres2),
+ & nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
+ & nlor_sccor(ntyp,ntyp)
+
--- /dev/null
+C Parameters of the SC rotamers (local) term
+ double precision sc_parmin
+ common/scrot/sc_parmin(maxsccoef,20)
--- /dev/null
+ DOUBLE PRECISION BATIME,TIMLIM,STIME,PREVTIM,SAFETY,RSTIME
+ INTEGER WhatsUp,ndelta
+ logical cutoffviol,cutoffeval,llocal
+ COMMON/TIME1/STIME,TIMLIM,BATIME,PREVTIM,SAFETY,RSTIME
+ COMMON/STOPTIM/WhatsUp,ndelta,cutoffviol,cutoffeval,llocal
+ double precision t_func,t_grad,t_fhel,t_fbet,t_ghel,t_gbet,t_viol,
+ & t_gviol,t_map,t_alamap,t_betamap
+ integer n_func,n_grad,n_fhel,n_fbet,n_ghel,n_gbet,n_viol,n_gviol,
+ & n_map,n_alamap,n_betamap
+ common /timing/ t_func,t_grad,t_fhel,t_fbet,t_ghel,t_gbet,t_viol,
+ & t_gviol,t_map,t_alamap,t_betamap,
+ & n_func,n_grad,n_fhel,n_fbet,n_ghel,n_gbet,n_viol,n_gviol,
+ & n_map,n_alamap,n_betamap
--- /dev/null
+ integer ndih_constr,idih_constr(maxdih_constr)
+ integer ndih_nconstr,idih_nconstr(maxdih_constr)
+ double precision phi0(maxdih_constr),drange(maxdih_constr),ftors
+ common /torcnstr/ phi0,drange,ftors,ndih_constr,idih_constr,
+ & ndih_nconstr,idih_nconstr
--- /dev/null
+C Torsional constants of the rotation about virtual-bond dihedral angles
+ double precision v1,v2,vlor1,vlor2,vlor3,v0
+ integer itortyp,ntortyp,nterm,nlor,nterm_old
+ common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
+ & v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
+ & vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
+ & itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor)
+ & ,nterm_old
+C 6/23/01 - constants for double torsionals
+ double precision v1c,v1s,v2c,v2s
+ integer ntermd_1,ntermd_2
+ common /torsiond/ v1c(2,maxtermd_1,maxtor,maxtor,maxtor),
+ & v1s(2,maxtermd_1,maxtor,maxtor,maxtor),
+ & v2c(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
+ & v2s(maxtermd_2,maxtermd_2,maxtor,maxtor,maxtor),
+ & ntermd_1(maxtor,maxtor,maxtor),ntermd_2(maxtor,maxtor,maxtor)
+C 9/18/99 - added Fourier coeffficients of the expansion of local energy
+C surface
+ double precision b1,b2,cc,dd,ee,ctilde,dtilde,b1tilde,
+ & bnew1,bnew2,eenew,eeold
+ integer nloctyp
+ common/fourier/ b1(2,maxtor),b2(2,maxtor),
+ & bnew1(3,2,maxtor),bnew2(3,2,maxtor),
+ & cc(2,2,maxtor),
+ & dd(2,2,maxtor),eeold(2,2,maxtor),eenew(2,maxtor),
+ & ee(2,2,maxtor),ctilde(2,2,maxtor),dtilde(2,2,maxtor),
+ & b1tilde(2,maxtor),nloctyp
+ double precision b
+ common /fourier1/ b(13,maxtor)
--- /dev/null
+C Store the geometric variables in the following COMMON block.
+ integer ntheta,nphi,nside,nvar,Origin,nstore,ialph,ivar,
+ & mask_theta,mask_phi,mask_side
+ double precision theta,phi,alph,omeg,varsave,esave,varall,vbld,
+ & thetaref,phiref,costtab,sinttab,cost2tab,sint2tab,
+ & xxtab,yytab,zztab,xxref,yyref,zzref
+ common /var/ theta(maxres),phi(maxres),alph(maxres),omeg(maxres),
+ & omicron(2,maxres),tauangle(3,maxres),
+ & vbld(2*maxres),thetaref(maxres),phiref(maxres),
+ & costtab(maxres), sinttab(maxres), cost2tab(maxres),
+ & sint2tab(maxres),xxtab(maxres),yytab(maxres),
+ & zztab(maxres),xxref(maxres),yyref(maxres),zzref(maxres),
+ & ialph(maxres,2),ivar(4*maxres2),ntheta,nphi,nside,nvar
+C Store the angles and variables corresponding to old conformations (for use
+C in MCM).
+ common /oldgeo/ varsave(maxvar,maxsave),esave(maxsave),
+ & Origin(maxsave),nstore
+C freeze some variables
+ logical mask_r
+ common /restr/ varall(maxvar),mask_r,mask_theta(maxres),
+ & mask_phi(maxres),mask_side(maxres)
--- /dev/null
+ common /vectors/ uy(3,maxres),uz(3,maxres),
+ & uygrad(3,3,2,maxres),uzgrad(3,3,2,maxres)
+
--- /dev/null
+ double precision ww,ww0,ww_low,ww_up,ww_orig,x_orig,
+ & epp_low,epp_up,rpp_low,rpp_up,elpp6_low,elpp6_up,elpp3_low,
+ & elpp3_up,b_low,b_up,epscp_low,epscp_up,rscp_low,rscp_up,
+ & x_up,x_low,xm,xm1,xm2,epss_low,epss_up,epsp_low,epsp_up
+ integer imask,mask_elec,mask_fourier,mod_fourier,mask_scp,indz,iw,
+ & nsingle_sc,npair_sc,ityp_ssc,ityp_psc
+ logical mod_other_params,mod_elec,mod_scp,mod_side
+ common /chujec/ ww(max_ene),ww0(max_ene),ww_low(max_ene),
+ & ww_up(max_ene),ww_orig(max_ene),x_orig(max_paropt),
+ & epp_low(2,2),epp_up(2,2),rpp_low(2,2),rpp_up(2,2),
+ & elpp6_low(2,2),elpp6_up(2,2),elpp3_low(2,2),elpp3_up(2,2),
+ & b_low(13,3),b_up(13,3),x_up(max_paropt),x_low(max_paropt),
+ & epscp_low(0:20,2),epscp_up(0:20,2),rscp_low(0:20,2),
+ & rscp_up(0:20,2),epss_low(ntyp),epss_up(ntyp),epsp_low(nntyp),
+ & epsp_up(nntyp),
+ & xm(max_paropt,0:maxprot),xm1(max_paropt,0:maxprot),
+ & xm2(max_paropt,0:maxprot),
+ & imask(max_ene),nsingle_sc,npair_sc,ityp_ssc(ntyp),
+ & ityp_psc(2,nntyp),mask_elec(2,2,4),
+ & mask_fourier(13,3),
+ & mask_scp(0:20,2,2),mod_other_params,mod_fourier(0:3),
+ & mod_elec,mod_scp,mod_side,indz(maxbatch+1,maxprot),iw(max_ene)
--- /dev/null
+ subroutine initialize
+C
+C Define constants and zero out tables.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.MINIM'
+ include 'COMMON.DERIV'
+ include "COMMON.WEIGHTS"
+ include "COMMON.NAMES"
+ include "COMMON.TIME1"
+C
+C The following is just to define auxiliary variables used in angle conversion
+C
+ pi=4.0D0*datan(1.0D0)
+ dwapi=2.0D0*pi
+ dwapi3=dwapi/3.0D0
+ pipol=0.5D0*pi
+ deg2rad=pi/180.0D0
+ rad2deg=1.0D0/deg2rad
+ angmin=10.0D0*deg2rad
+C
+C Define I/O units.
+C
+ inp= 1
+ iout= 2
+ ipdbin= 3
+ ipdb= 7
+ imol2= 4
+ igeom= 8
+ intin= 9
+ ithep= 11
+ irotam=12
+ itorp= 13
+ itordp= 23
+ ielep= 14
+ isidep=15
+ isidep1=22
+ iscpp=25
+ icbase=16
+ ifourier=20
+ istat= 17
+ ientin=18
+ ientout=19
+ ibond=28
+ isccor=29
+C
+C WHAM files
+C
+ ihist=30
+ iweight=31
+ izsc=32
+C
+C Set default weights of the energy terms.
+C
+ wlong=1.0D0
+ welec=1.0D0
+ wtor =1.0D0
+ wang =1.0D0
+ wscloc=1.0D0
+ wstrain=1.0D0
+C
+C Zero out tables.
+C
+ ndih_constr=0
+ do i=1,maxres2
+ do j=1,3
+ c(j,i)=0.0D0
+ dc(j,i)=0.0D0
+ enddo
+ enddo
+ do i=1,maxres
+ do j=1,3
+ xloc(j,i)=0.0D0
+ enddo
+ enddo
+ do i=1,ntyp
+ do j=1,ntyp
+ aa(i,j)=0.0D0
+ bb(i,j)=0.0D0
+ augm(i,j)=0.0D0
+ sigma(i,j)=0.0D0
+ r0(i,j)=0.0D0
+ chi(i,j)=0.0D0
+ enddo
+ do j=1,2
+ bad(i,j)=0.0D0
+ enddo
+ chip(i)=0.0D0
+ alp(i)=0.0D0
+ sigma0(i)=0.0D0
+ sigii(i)=0.0D0
+ rr0(i)=0.0D0
+ a0thet(i)=0.0D0
+ do j=1,2
+ athet(j,i)=0.0D0
+ bthet(j,i)=0.0D0
+ enddo
+ do j=0,3
+ polthet(j,i)=0.0D0
+ enddo
+ do j=1,3
+ gthet(j,i)=0.0D0
+ enddo
+ theta0(i)=0.0D0
+ sig0(i)=0.0D0
+ sigc0(i)=0.0D0
+ do j=1,maxlob
+ bsc(j,i)=0.0D0
+ do k=1,3
+ censc(k,j,i)=0.0D0
+ enddo
+ do k=1,3
+ do l=1,3
+ gaussc(l,k,j,i)=0.0D0
+ enddo
+ enddo
+ nlob(i)=0
+ enddo
+ enddo
+ nlob(ntyp1)=0
+ dsc(ntyp1)=0.0D0
+ do i=1,maxtor
+ itortyp(i)=0
+ do j=1,maxtor
+ do k=1,maxterm
+ v1(k,j,i)=0.0D0
+ v2(k,j,i)=0.0D0
+ enddo
+ enddo
+ enddo
+ do i=1,maxres
+ itype(i)=0
+ itel(i)=0
+ enddo
+C Initialize the bridge arrays
+ ns=0
+ nss=0
+ nhpb=0
+ do i=1,maxss
+ iss(i)=0
+ enddo
+ do i=1,maxdim
+ dhpb(i)=0.0D0
+ enddo
+ do i=1,maxres
+ ihpb(i)=0
+ jhpb(i)=0
+ enddo
+C
+C Initialize timing.
+C
+ call set_timers
+C
+C Initialize variables used in minimization.
+C
+c maxfun=5000
+c maxit=2000
+ maxfun=500
+ maxit=200
+ tolf=1.0D-2
+ rtolf=5.0D-4
+C
+C Initialize the variables responsible for the mode of gradient storage.
+C
+ nfl=0
+ icg=1
+ do i=1,14
+ do j=1,14
+ if (print_order(i).eq.j) then
+ iw(print_order(i))=j
+ goto 1121
+ endif
+ enddo
+1121 continue
+ enddo
+ calc_grad=.false.
+C Set timers and counters for the respective routines
+ t_func = 0.0d0
+ t_grad = 0.0d0
+ t_fhel = 0.0d0
+ t_fbet = 0.0d0
+ t_ghel = 0.0d0
+ t_gbet = 0.0d0
+ t_viol = 0.0d0
+ t_gviol = 0.0d0
+ n_func = 0
+ n_grad = 0
+ n_fhel = 0
+ n_fbet = 0
+ n_ghel = 0
+ n_gbet = 0
+ n_viol = 0
+ n_gviol = 0
+ n_map = 0
+#ifndef SPLITELE
+ nprint_ene=nprint_ene-1
+#endif
+ return
+ end
+c-------------------------------------------------------------------------
+ block data nazwy
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.NAMES'
+ include 'COMMON.WEIGHTS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.INTERACT'
+ data restyp /
+ &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
+ &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
+ data onelet /
+ &'C','M','F','I','L','V','W','Y','A','G','T',
+ &'S','Q','N','E','D','H','R','K','P','X'/
+ data potname /'LJ','LJK','BP','GB','GBV','MM'/
+ data ename /
+ & "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ",
+ & "ECORR6 ","EELLO ","ETURN3 ","ETURN4 ","ETURN6 ",
+ & "EBE bend","ESC SCloc","ETORS ","ETORSD ","EHPB","EVDWPP",
+ & "EVDW2_14","ESTR","ESCCOR","EDIHC","EVDW_T"/
+ data wname /
+ & "WSC","WSCP","WELEC","WCORR","WCORR5","WCORR6","WEL_LOC",
+ & "WTURN3","WTURN4","WTURN6","WANG","WSCLOC","WTOR","WTORD",
+ & "WHPB","WVDWPP","WSCP14","WBOND","WSCCOR","WDIHC","WSC"/
+ data ww0 /1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,
+ & 1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,1.0d0,0.4d0,1.0d0,1.0d0,
+ & 0.0d0,0.0/
+ data nprint_ene /21/
+ data print_order /1,2,3,18,11,12,13,14,4,5,6,7,8,9,10,19,
+ & 16,15,17,20,21/
+c Dielectric constant of water
+ data eps_out /80.0d0/
+ end
+c---------------------------------------------------------------------------
+ subroutine init_int_table
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+#ifdef MP
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+ logical scheck,lprint
+#ifdef MPL
+ integer my_sc_int(0:max_fg_Procs-1),my_sc_intt(0:max_fg_Procs),
+ & my_ele_int(0:max_fg_Procs-1),my_ele_intt(0:max_fg_Procs)
+C... Determine the numbers of start and end SC-SC interaction
+C... to deal with by current processor.
+ lprint=.false.
+ if (lprint)
+ &write (iout,*) 'INIT_INT_TABLE nres=',nres,' nnt=',nnt,' nct=',nct
+ n_sc_int_tot=(nct-nnt+1)*(nct-nnt)/2-nss
+ MyRank=MyID-(MyGroup-1)*fgProcs
+ call int_bounds(n_sc_int_tot,my_sc_inds,my_sc_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' n_sc_int_tot',n_sc_int_tot,' my_sc_inds=',my_sc_inds,
+ & ' my_sc_inde',my_sc_inde
+ ind_sctint=0
+ iatsc_s=0
+ iatsc_e=0
+#endif
+ lprint=.false.
+ do i=1,maxres
+ nint_gr(i)=0
+ nscp_gr(i)=0
+ do j=1,maxint_gr
+ istart(i,1)=0
+ iend(i,1)=0
+ ielstart(i)=0
+ ielend(i)=0
+ iscpstart(i,1)=0
+ iscpend(i,1)=0
+ enddo
+ enddo
+ ind_scint=0
+ ind_scint_old=0
+cd write (iout,*) 'ns=',ns,' nss=',nss,' ihpb,jhpb',
+cd & (ihpb(i),jhpb(i),i=1,nss)
+ do i=nnt,nct-1
+ scheck=.false.
+ do ii=1,nss
+ if (ihpb(ii).eq.i+nres) then
+ scheck=.true.
+ jj=jhpb(ii)-nres
+ goto 10
+ endif
+ enddo
+ 10 continue
+cd write (iout,*) 'i=',i,' scheck=',scheck,' jj=',jj
+ if (scheck) then
+ if (jj.eq.i+1) then
+#ifdef MPL
+ write (iout,*) 'jj=i+1'
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+2,nct,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+2
+ iend(i,1)=nct
+#endif
+ else if (jj.eq.nct) then
+#ifdef MPL
+ write (iout,*) 'jj=nct'
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,nct-1,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+1
+ iend(i,1)=nct-1
+#endif
+ else
+#ifdef MPL
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,jj-1,nint_gr(i),istart(i,1),iend(i,1),*12)
+ ii=nint_gr(i)+1
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,jj+1,nct,nint_gr(i),istart(i,ii),iend(i,ii),*12)
+#else
+ nint_gr(i)=2
+ istart(i,1)=i+1
+ iend(i,1)=jj-1
+ istart(i,2)=jj+1
+ iend(i,2)=nct
+#endif
+ endif
+ else
+#ifdef MPL
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,nct,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+1
+ iend(i,1)=nct
+ ind_scint=int_scint+nct-i
+#endif
+ endif
+#ifdef MPL
+ ind_scint_old=ind_scint
+#endif
+ enddo
+ 12 continue
+#ifndef MPL
+ iatsc_s=nnt
+ iatsc_e=nct-1
+#endif
+#ifdef MPL
+ if (lprint) then
+ write (iout,*) 'Processor',MyID,' Group',MyGroup
+ write (iout,*) 'iatsc_s=',iatsc_s,' iatsc_e=',iatsc_e
+ endif
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'Interaction array:'
+ do i=iatsc_s,iatsc_e
+ write (iout,'(i3,2(2x,2i3))')
+ & i,(istart(i,iint),iend(i,iint),iint=1,nint_gr(i))
+ enddo
+ endif
+ ispp=2
+#ifdef MPL
+C Now partition the electrostatic-interaction array
+ npept=nct-nnt
+ nele_int_tot=(npept-ispp)*(npept-ispp+1)/2
+ call int_bounds(nele_int_tot,my_ele_inds,my_ele_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' nele_int_tot',nele_int_tot,' my_ele_inds=',my_ele_inds,
+ & ' my_ele_inde',my_ele_inde
+ iatel_s=0
+ iatel_e=0
+ ind_eleint=0
+ ind_eleint_old=0
+ do i=nnt,nct-3
+ ijunk=0
+ call int_partition(ind_eleint,my_ele_inds,my_ele_inde,i,
+ & iatel_s,iatel_e,i+ispp,nct-1,ijunk,ielstart(i),ielend(i),*13)
+ enddo ! i
+ 13 continue
+#else
+ iatel_s=nnt
+ iatel_e=nct-3
+ do i=iatel_s,iatel_e
+ ielstart(i)=i+2
+ ielend(i)=nct-1
+ enddo
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'Electrostatic interaction array:'
+ do i=iatel_s,iatel_e
+ write (iout,'(i3,2(2x,2i3))') i,ielstart(i),ielend(i)
+ enddo
+ endif ! lprint
+c iscp=3
+ iscp=2
+C Partition the SC-p interaction array
+#ifdef MPL
+ nscp_int_tot=(npept-iscp+1)*(npept-iscp+1)
+ call int_bounds(nscp_int_tot,my_scp_inds,my_scp_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' nscp_int_tot',nscp_int_tot,' my_scp_inds=',my_scp_inds,
+ & ' my_scp_inde',my_scp_inde
+ iatscp_s=0
+ iatscp_e=0
+ ind_scpint=0
+ ind_scpint_old=0
+ do i=nnt,nct-1
+ if (i.lt.nnt+iscp) then
+cd write (iout,*) 'i.le.nnt+iscp'
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,i+iscp,nct,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ else if (i.gt.nct-iscp) then
+cd write (iout,*) 'i.gt.nct-iscp'
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,nnt,i-iscp,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ else
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,nnt,i-iscp,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ ii=nscp_gr(i)+1
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,i+iscp,nct,nscp_gr(i),iscpstart(i,ii),
+ & iscpend(i,ii),*14)
+ endif
+ enddo ! i
+ 14 continue
+#else
+ iatscp_s=nnt
+ iatscp_e=nct-1
+ do i=nnt,nct-1
+ if (i.lt.nnt+iscp) then
+ nscp_gr(i)=1
+ iscpstart(i,1)=i+iscp
+ iscpend(i,1)=nct
+ elseif (i.gt.nct-iscp) then
+ nscp_gr(i)=1
+ iscpstart(i,1)=nnt
+ iscpend(i,1)=i-iscp
+ else
+ nscp_gr(i)=2
+ iscpstart(i,1)=nnt
+ iscpend(i,1)=i-iscp
+ iscpstart(i,2)=i+iscp
+ iscpend(i,2)=nct
+ endif
+ enddo ! i
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'SC-p interaction array:'
+ do i=iatscp_s,iatscp_e
+ write (iout,'(i3,2(2x,2i3))')
+ & i,(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
+ enddo
+ endif ! lprint
+C Partition local interactions
+#ifdef MPL
+ call int_bounds(nres-2,loc_start,loc_end)
+ loc_start=loc_start+1
+ loc_end=loc_end+1
+ call int_bounds(nres-2,ithet_start,ithet_end)
+ ithet_start=ithet_start+2
+ ithet_end=ithet_end+2
+ call int_bounds(nct-nnt-2,iphi_start,iphi_end)
+ iphi_start=iphi_start+nnt+2
+ iphi_end=iphi_end+nnt+2
+ call int_bounds(nres-3,itau_start,itau_end)
+ itau_start=itau_start+3
+ itau_end=itau_end+3
+ if (lprint) then
+ write (iout,*) 'Processor:',MyID,
+ & ' loc_start',loc_start,' loc_end',loc_end,
+ & ' ithet_start',ithet_start,' ithet_end',ithet_end,
+ & ' iphi_start',iphi_start,' iphi_end',iphi_end
+ write (*,*) 'Processor:',MyID,
+ & ' loc_start',loc_start,' loc_end',loc_end,
+ & ' ithet_start',ithet_start,' ithet_end',ithet_end,
+ & ' iphi_start',iphi_start,' iphi_end',iphi_end
+ endif
+ if (fgprocs.gt.1 .and. MyID.eq.BossID) then
+ write(iout,'(i10,a,i10,a,i10,a/a,i3,a)') n_sc_int_tot,' SC-SC ',
+ & nele_int_tot,' electrostatic and ',nscp_int_tot,
+ & ' SC-p interactions','were distributed among',fgprocs,
+ & ' fine-grain processors.'
+ endif
+#else
+ loc_start=2
+ loc_end=nres-1
+ ithet_start=3
+ ithet_end=nres
+ iphi_start=nnt+3
+ iphi_end=nct
+ itau_start=4
+ itau_end=nres
+#endif
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine int_partition(int_index,lower_index,upper_index,atom,
+ & at_start,at_end,first_atom,last_atom,int_gr,jat_start,jat_end,*)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ integer int_index,lower_index,upper_index,atom,at_start,at_end,
+ & first_atom,last_atom,int_gr,jat_start,jat_end
+ logical lprn
+ lprn=.false.
+ if (lprn) write (iout,*) 'int_index=',int_index
+ int_index_old=int_index
+ int_index=int_index+last_atom-first_atom+1
+ if (lprn)
+ & write (iout,*) 'int_index=',int_index,
+ & ' int_index_old',int_index_old,
+ & ' lower_index=',lower_index,
+ & ' upper_index=',upper_index,
+ & ' atom=',atom,' first_atom=',first_atom,
+ & ' last_atom=',last_atom
+ if (int_index.ge.lower_index) then
+ int_gr=int_gr+1
+ if (at_start.eq.0) then
+ at_start=atom
+ jat_start=first_atom-1+lower_index-int_index_old
+ else
+ jat_start=first_atom
+ endif
+ if (lprn) write (iout,*) 'jat_start',jat_start
+ if (int_index.ge.upper_index) then
+ at_end=atom
+ jat_end=first_atom-1+upper_index-int_index_old
+ return1
+ else
+ jat_end=last_atom
+ endif
+ if (lprn) write (iout,*) 'jat_end',jat_end
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine hpb_partition
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+ call int_bounds(nhpb,link_start,link_end)
+#else
+ link_start=1
+ link_end=nhpb
+#endif
+cd write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+cd & ' nhpb',nhpb,' link_start=',link_start,
+cd & ' link_end',link_end
+ return
+ end
--- /dev/null
+ subroutine initialize
+C
+C Define constants and zero out tables.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.MINIM'
+ include 'COMMON.DERIV'
+ include "COMMON.WEIGHTS"
+ include "COMMON.NAMES"
+ include "COMMON.TIME1"
+C
+C The following is just to define auxiliary variables used in angle conversion
+C
+ pi=4.0D0*datan(1.0D0)
+ dwapi=2.0D0*pi
+ dwapi3=dwapi/3.0D0
+ pipol=0.5D0*pi
+ deg2rad=pi/180.0D0
+ rad2deg=1.0D0/deg2rad
+ angmin=10.0D0*deg2rad
+C
+C Define I/O units.
+C
+ inp= 1
+ iout= 2
+ ipdbin= 3
+ ipdb= 7
+ imol2= 4
+ igeom= 8
+ intin= 9
+ ithep= 11
+ irotam=12
+ itorp= 13
+ itordp= 23
+ ielep= 14
+ isidep=15
+ iscpp=25
+ icbase=16
+ ifourier=20
+ istat= 17
+ ientin=18
+ ientout=19
+C
+C CSA I/O units (separated from others especially for Jooyoung)
+C
+ icsa_rbank=30
+ icsa_seed=31
+ icsa_history=32
+ icsa_bank=33
+ icsa_bank1=34
+ icsa_alpha=35
+ icsa_alpha1=36
+ icsa_bankt=37
+ icsa_int=39
+ icsa_bank_reminimized=38
+ icsa_native_int=41
+ icsa_in=40
+C
+C Set default weights of the energy terms.
+C
+ wlong=1.0D0
+ welec=1.0D0
+ wtor =1.0D0
+ wang =1.0D0
+ wscloc=1.0D0
+ wstrain=1.0D0
+C
+C Zero out tables.
+C
+ ndih_constr=0
+ do i=1,maxres2
+ do j=1,3
+ c(j,i)=0.0D0
+ dc(j,i)=0.0D0
+ enddo
+ enddo
+ do i=1,maxres
+ do j=1,3
+ xloc(j,i)=0.0D0
+ enddo
+ enddo
+ do i=1,ntyp
+ do j=1,ntyp
+ aa(i,j)=0.0D0
+ bb(i,j)=0.0D0
+ augm(i,j)=0.0D0
+ sigma(i,j)=0.0D0
+ r0(i,j)=0.0D0
+ chi(i,j)=0.0D0
+ enddo
+ do j=1,2
+ bad(i,j)=0.0D0
+ enddo
+ chip(i)=0.0D0
+ alp(i)=0.0D0
+ sigma0(i)=0.0D0
+ sigii(i)=0.0D0
+ rr0(i)=0.0D0
+ a0thet(i)=0.0D0
+ do j=1,2
+ athet(j,i)=0.0D0
+ bthet(j,i)=0.0D0
+ enddo
+ do j=0,3
+ polthet(j,i)=0.0D0
+ enddo
+ do j=1,3
+ gthet(j,i)=0.0D0
+ enddo
+ theta0(i)=0.0D0
+ sig0(i)=0.0D0
+ sigc0(i)=0.0D0
+ do j=1,maxlob
+ bsc(j,i)=0.0D0
+ do k=1,3
+ censc(k,j,i)=0.0D0
+ enddo
+ do k=1,3
+ do l=1,3
+ gaussc(l,k,j,i)=0.0D0
+ enddo
+ enddo
+ nlob(i)=0
+ enddo
+ enddo
+ nlob(ntyp1)=0
+ dsc(ntyp1)=0.0D0
+ do i=1,maxtor
+ itortyp(i)=0
+ do j=1,maxtor
+ do k=1,maxterm
+ v1(k,j,i)=0.0D0
+ v2(k,j,i)=0.0D0
+ enddo
+ enddo
+ enddo
+ do i=1,maxres
+ itype(i)=0
+ itel(i)=0
+ enddo
+C Initialize the bridge arrays
+ ns=0
+ nss=0
+ nhpb=0
+ do i=1,maxss
+ iss(i)=0
+ enddo
+ do i=1,maxdim
+ dhpb(i)=0.0D0
+ enddo
+ do i=1,maxres
+ ihpb(i)=0
+ jhpb(i)=0
+ enddo
+C
+C Initialize timing.
+C
+ call set_timers
+C
+C Initialize variables used in minimization.
+C
+c maxfun=5000
+c maxit=2000
+ maxfun=500
+ maxit=200
+ tolf=1.0D-2
+ rtolf=5.0D-4
+C
+C Initialize the variables responsible for the mode of gradient storage.
+C
+ nfl=0
+ icg=1
+ do i=1,14
+ do j=1,14
+ if (print_order(i).eq.j) then
+ iw(print_order(i))=j
+ goto 1121
+ endif
+ enddo
+1121 continue
+ enddo
+ calc_grad=.false.
+C Set timers and counters for the respective routines
+ t_func = 0.0d0
+ t_grad = 0.0d0
+ t_fhel = 0.0d0
+ t_fbet = 0.0d0
+ t_ghel = 0.0d0
+ t_gbet = 0.0d0
+ t_viol = 0.0d0
+ t_gviol = 0.0d0
+ n_func = 0
+ n_grad = 0
+ n_fhel = 0
+ n_fbet = 0
+ n_ghel = 0
+ n_gbet = 0
+ n_viol = 0
+ n_gviol = 0
+ n_map = 0
+ return
+ end
+c-------------------------------------------------------------------------
+ block data nazwy
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.NAMES'
+ include 'COMMON.FFIELD'
+ data restyp /
+ &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
+ &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
+ data onelet /
+ &'C','M','F','I','L','V','W','Y','A','G','T',
+ &'S','Q','N','E','D','H','R','K','P','X'/
+ data potname /'LJ','LJK','BP','GB','GBV'/
+ data ename /
+ & "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ",
+ & "ECORR6 ","EELLO ","ETURN3 ","ETURN4 ","ETURN6 ",
+ & "EBE bend","ESC SCloc","ETORS ","ETORSD ","EVDW2_14",2*" "/
+ data wname /
+ & "WSC","WSCP","WELEC","WCORR","WCORR5","WCORR6","WEL_LOC",
+ & "WTURN3","WTURN4","WTURN6","WANG","WSCLOC","WTOR","WTORD",
+ & "SCAL14",2*" "/
+#ifdef SCP14
+ data nprint_ene /15/
+ data print_order /1,2,3,11,12,13,14,4,5,6,7,8,9,10,16,0/
+#else
+ data nprint_ene /14/
+ data print_order /1,2,3,11,12,13,14,4,5,6,7,8,9,10,3*0/
+#endif
+ end
+c---------------------------------------------------------------------------
+ subroutine init_int_table
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+#ifdef MP
+ include 'COMMON.INFO'
+#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+ logical scheck,lprint
+#ifdef MPL
+ integer my_sc_int(0:max_fg_Procs-1),my_sc_intt(0:max_fg_Procs),
+ & my_ele_int(0:max_fg_Procs-1),my_ele_intt(0:max_fg_Procs)
+C... Determine the numbers of start and end SC-SC interaction
+C... to deal with by current processor.
+ lprint=.false.
+ if (lprint)
+ &write (iout,*) 'INIT_INT_TABLE nres=',nres,' nnt=',nnt,' nct=',nct
+ n_sc_int_tot=(nct-nnt+1)*(nct-nnt)/2-nss
+ MyRank=MyID-(MyGroup-1)*fgProcs
+ call int_bounds(n_sc_int_tot,my_sc_inds,my_sc_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' n_sc_int_tot',n_sc_int_tot,' my_sc_inds=',my_sc_inds,
+ & ' my_sc_inde',my_sc_inde
+ ind_sctint=0
+ iatsc_s=0
+ iatsc_e=0
+#endif
+ lprint=.false.
+ do i=1,maxres
+ nint_gr(i)=0
+ nscp_gr(i)=0
+ do j=1,maxint_gr
+ istart(i,1)=0
+ iend(i,1)=0
+ ielstart(i)=0
+ ielend(i)=0
+ iscpstart(i,1)=0
+ iscpend(i,1)=0
+ enddo
+ enddo
+ ind_scint=0
+ ind_scint_old=0
+cd write (iout,*) 'ns=',ns,' nss=',nss,' ihpb,jhpb',
+cd & (ihpb(i),jhpb(i),i=1,nss)
+ do i=nnt,nct-1
+ scheck=.false.
+ do ii=1,nss
+ if (ihpb(ii).eq.i+nres) then
+ scheck=.true.
+ jj=jhpb(ii)-nres
+ goto 10
+ endif
+ enddo
+ 10 continue
+cd write (iout,*) 'i=',i,' scheck=',scheck,' jj=',jj
+ if (scheck) then
+ if (jj.eq.i+1) then
+#ifdef MPL
+ write (iout,*) 'jj=i+1'
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+2,nct,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+2
+ iend(i,1)=nct
+#endif
+ else if (jj.eq.nct) then
+#ifdef MPL
+ write (iout,*) 'jj=nct'
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,nct-1,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+1
+ iend(i,1)=nct-1
+#endif
+ else
+#ifdef MPL
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,jj-1,nint_gr(i),istart(i,1),iend(i,1),*12)
+ ii=nint_gr(i)+1
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,jj+1,nct,nint_gr(i),istart(i,ii),iend(i,ii),*12)
+#else
+ nint_gr(i)=2
+ istart(i,1)=i+1
+ iend(i,1)=jj-1
+ istart(i,2)=jj+1
+ iend(i,2)=nct
+#endif
+ endif
+ else
+#ifdef MPL
+ call int_partition(ind_scint,my_sc_inds,my_sc_inde,i,
+ & iatsc_s,iatsc_e,i+1,nct,nint_gr(i),istart(i,1),iend(i,1),*12)
+#else
+ nint_gr(i)=1
+ istart(i,1)=i+1
+ iend(i,1)=nct
+ ind_scint=int_scint+nct-i
+#endif
+ endif
+#ifdef MPL
+ ind_scint_old=ind_scint
+#endif
+ enddo
+ 12 continue
+#ifndef MPL
+ iatsc_s=nnt
+ iatsc_e=nct-1
+#endif
+#ifdef MPL
+ if (lprint) then
+ write (iout,*) 'Processor',MyID,' Group',MyGroup
+ write (iout,*) 'iatsc_s=',iatsc_s,' iatsc_e=',iatsc_e
+ endif
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'Interaction array:'
+ do i=iatsc_s,iatsc_e
+ write (iout,'(i3,2(2x,2i3))')
+ & i,(istart(i,iint),iend(i,iint),iint=1,nint_gr(i))
+ enddo
+ endif
+ ispp=2
+#ifdef MPL
+C Now partition the electrostatic-interaction array
+ npept=nct-nnt
+ nele_int_tot=(npept-ispp)*(npept-ispp+1)/2
+ call int_bounds(nele_int_tot,my_ele_inds,my_ele_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' nele_int_tot',nele_int_tot,' my_ele_inds=',my_ele_inds,
+ & ' my_ele_inde',my_ele_inde
+ iatel_s=0
+ iatel_e=0
+ ind_eleint=0
+ ind_eleint_old=0
+ do i=nnt,nct-3
+ ijunk=0
+ call int_partition(ind_eleint,my_ele_inds,my_ele_inde,i,
+ & iatel_s,iatel_e,i+ispp,nct-1,ijunk,ielstart(i),ielend(i),*13)
+ enddo ! i
+ 13 continue
+#else
+ iatel_s=nnt
+ iatel_e=nct-3
+ do i=iatel_s,iatel_e
+ ielstart(i)=i+2
+ ielend(i)=nct-1
+ enddo
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'Electrostatic interaction array:'
+ do i=iatel_s,iatel_e
+ write (iout,'(i3,2(2x,2i3))') i,ielstart(i),ielend(i)
+ enddo
+ endif ! lprint
+c iscp=3
+ iscp=2
+C Partition the SC-p interaction array
+#ifdef MPL
+ nscp_int_tot=(npept-iscp+1)*(npept-iscp+1)
+ call int_bounds(nscp_int_tot,my_scp_inds,my_scp_inde)
+ if (lprint)
+ & write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+ & ' nscp_int_tot',nscp_int_tot,' my_scp_inds=',my_scp_inds,
+ & ' my_scp_inde',my_scp_inde
+ iatscp_s=0
+ iatscp_e=0
+ ind_scpint=0
+ ind_scpint_old=0
+ do i=nnt,nct-1
+ if (i.lt.nnt+iscp) then
+cd write (iout,*) 'i.le.nnt+iscp'
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,i+iscp,nct,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ else if (i.gt.nct-iscp) then
+cd write (iout,*) 'i.gt.nct-iscp'
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,nnt,i-iscp,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ else
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,nnt,i-iscp,nscp_gr(i),iscpstart(i,1),
+ & iscpend(i,1),*14)
+ ii=nscp_gr(i)+1
+ call int_partition(ind_scpint,my_scp_inds,my_scp_inde,i,
+ & iatscp_s,iatscp_e,i+iscp,nct,nscp_gr(i),iscpstart(i,ii),
+ & iscpend(i,ii),*14)
+ endif
+ enddo ! i
+ 14 continue
+#else
+ iatscp_s=nnt
+ iatscp_e=nct-1
+ do i=nnt,nct-1
+ if (i.lt.nnt+iscp) then
+ nscp_gr(i)=1
+ iscpstart(i,1)=i+iscp
+ iscpend(i,1)=nct
+ elseif (i.gt.nct-iscp) then
+ nscp_gr(i)=1
+ iscpstart(i,1)=nnt
+ iscpend(i,1)=i-iscp
+ else
+ nscp_gr(i)=2
+ iscpstart(i,1)=nnt
+ iscpend(i,1)=i-iscp
+ iscpstart(i,2)=i+iscp
+ iscpend(i,2)=nct
+ endif
+ enddo ! i
+#endif
+ if (lprint) then
+ write (iout,'(a)') 'SC-p interaction array:'
+ do i=iatscp_s,iatscp_e
+ write (iout,'(i3,2(2x,2i3))')
+ & i,(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
+ enddo
+ endif ! lprint
+C Partition local interactions
+#ifdef MPL
+ call int_bounds(nres-2,loc_start,loc_end)
+ loc_start=loc_start+1
+ loc_end=loc_end+1
+ call int_bounds(nres-2,ithet_start,ithet_end)
+ ithet_start=ithet_start+2
+ ithet_end=ithet_end+2
+ call int_bounds(nct-nnt-2,iphi_start,iphi_end)
+ iphi_start=iphi_start+nnt+2
+ iphi_end=iphi_end+nnt+2
+ if (lprint) then
+ write (iout,*) 'Processor:',MyID,
+ & ' loc_start',loc_start,' loc_end',loc_end,
+ & ' ithet_start',ithet_start,' ithet_end',ithet_end,
+ & ' iphi_start',iphi_start,' iphi_end',iphi_end
+ write (*,*) 'Processor:',MyID,
+ & ' loc_start',loc_start,' loc_end',loc_end,
+ & ' ithet_start',ithet_start,' ithet_end',ithet_end,
+ & ' iphi_start',iphi_start,' iphi_end',iphi_end
+ endif
+ if (fgprocs.gt.1 .and. MyID.eq.BossID) then
+ write(iout,'(i10,a,i10,a,i10,a/a,i3,a)') n_sc_int_tot,' SC-SC ',
+ & nele_int_tot,' electrostatic and ',nscp_int_tot,
+ & ' SC-p interactions','were distributed among',fgprocs,
+ & ' fine-grain processors.'
+ endif
+#else
+ loc_start=2
+ loc_end=nres-1
+ ithet_start=3
+ ithet_end=nres
+ iphi_start=nnt+3
+ iphi_end=nct
+#endif
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine int_partition(int_index,lower_index,upper_index,atom,
+ & at_start,at_end,first_atom,last_atom,int_gr,jat_start,jat_end,*)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ integer int_index,lower_index,upper_index,atom,at_start,at_end,
+ & first_atom,last_atom,int_gr,jat_start,jat_end
+ logical lprn
+ lprn=.false.
+ if (lprn) write (iout,*) 'int_index=',int_index
+ int_index_old=int_index
+ int_index=int_index+last_atom-first_atom+1
+ if (lprn)
+ & write (iout,*) 'int_index=',int_index,
+ & ' int_index_old',int_index_old,
+ & ' lower_index=',lower_index,
+ & ' upper_index=',upper_index,
+ & ' atom=',atom,' first_atom=',first_atom,
+ & ' last_atom=',last_atom
+ if (int_index.ge.lower_index) then
+ int_gr=int_gr+1
+ if (at_start.eq.0) then
+ at_start=atom
+ jat_start=first_atom-1+lower_index-int_index_old
+ else
+ jat_start=first_atom
+ endif
+ if (lprn) write (iout,*) 'jat_start',jat_start
+ if (int_index.ge.upper_index) then
+ at_end=atom
+ jat_end=first_atom-1+upper_index-int_index_old
+ return1
+ else
+ jat_end=last_atom
+ endif
+ if (lprn) write (iout,*) 'jat_end',jat_end
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine hpb_partition
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+#ifdef MPL
+ include 'COMMON.INFO'
+ call int_bounds(nhpb,link_start,link_end)
+#else
+ link_start=1
+ link_end=nhpb
+#endif
+cd write (iout,*) 'Processor',MyID,' MyRank',MyRank,
+cd & ' nhpb',nhpb,' link_start=',link_start,
+cd & ' link_end',link_end
+ return
+ end
--- /dev/null
+ subroutine int_from_cart1(lprn)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.NAMES'
+ integer i,j
+ double precision dist,alpha,beta,dnorm1,dnorm2,be
+ logical lprn
+ if (lprn) write (iout,'(/a)') 'Recalculated internal coordinates'
+ vbld(nres+1)=0.0d0
+ vbld(2*nres)=0.0d0
+ vbld_inv(nres+1)=0.0d0
+ vbld_inv(2*nres)=0.0d0
+ do i=2,nres
+ dnorm1=dist(i-1,i)
+ dnorm2=dist(i,i+1)
+ do j=1,3
+ c(j,maxres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))/dnorm1
+ & +(c(j,i+1)-c(j,i))/dnorm2)
+ enddo
+ be=0.0D0
+ if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+ if (i.gt.2) tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
+ if (i.gt.2) tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
+ if (i.gt.2) tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
+
+ omeg(i)=beta(nres+i,i,maxres2,i+1)
+ theta(i+1)=alpha(i-1,i,i+1)
+ alph(i)=alpha(nres+i,i,maxres2)
+ vbld(i)=dist(i-1,i)
+ vbld_inv(i)=1.0d0/vbld(i)
+ vbld(nres+i)=dist(nres+i,i)
+ if (itype(i).ne.10) then
+ vbld_inv(nres+i)=1.0d0/vbld(nres+i)
+ else
+ vbld_inv(nres+i)=0.0d0
+ endif
+ enddo
+ do i=1,nres-1
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
+ enddo
+ enddo
+ do i=1,nres
+ do j=1,3
+ dc(j,i+nres)=c(j,i+nres)-c(j,i)
+ dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
+ enddo
+ enddo
+ if (lprn) then
+ do i=2,nres
+ write (iout,1212) restyp(itype(i)),i,vbld(i),
+ &rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),
+ &rad2deg*alph(i),rad2deg*omeg(i)
+ enddo
+ endif
+ 1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
+ return
+ end
--- /dev/null
+C
+C------------------------------------------------------------------------------
+C
+ double precision function alpha(i1,i2,i3)
+c
+c Calculates the planar angle between atoms (i1), (i2), and (i3).
+c
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.CHAIN'
+ x12=c(1,i1)-c(1,i2)
+ x23=c(1,i3)-c(1,i2)
+ y12=c(2,i1)-c(2,i2)
+ y23=c(2,i3)-c(2,i2)
+ z12=c(3,i1)-c(3,i2)
+ z23=c(3,i3)-c(3,i2)
+ vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
+ wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
+ scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
+ alpha=arcos(scalar)
+ return
+ end
+C
+C------------------------------------------------------------------------------
+C
+ double precision function beta(i1,i2,i3,i4)
+c
+c Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
+c
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.CHAIN'
+ x12=c(1,i1)-c(1,i2)
+ x23=c(1,i3)-c(1,i2)
+ x34=c(1,i4)-c(1,i3)
+ y12=c(2,i1)-c(2,i2)
+ y23=c(2,i3)-c(2,i2)
+ y34=c(2,i4)-c(2,i3)
+ z12=c(3,i1)-c(3,i2)
+ z23=c(3,i3)-c(3,i2)
+ z34=c(3,i4)-c(3,i3)
+cd print '(2i3,3f10.5)',i1,i2,x12,y12,z12
+cd print '(2i3,3f10.5)',i2,i3,x23,y23,z23
+cd print '(2i3,3f10.5)',i3,i4,x34,y34,z34
+ wx=-y23*z34+y34*z23
+ wy=x23*z34-z23*x34
+ wz=-x23*y34+y23*x34
+ wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
+ vx=y12*z23-z12*y23
+ vy=-x12*z23+z12*x23
+ vz=x12*y23-y12*x23
+ vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
+ if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
+ scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
+ if (dabs(scalar).gt.1.0D0)
+ &scalar=0.99999999999999D0*scalar/dabs(scalar)
+ angle=dacos(scalar)
+cd print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
+cd &scalar,angle
+ else
+ angle=pi
+ endif
+c if (angle.le.0.0D0) angle=pi+angle
+ tx=vy*wz-vz*wy
+ ty=-vx*wz+vz*wx
+ tz=vx*wy-vy*wx
+ scalar=tx*x23+ty*y23+tz*z23
+ if (scalar.lt.0.0D0) angle=-angle
+ beta=angle
+ return
+ end
+C
+C------------------------------------------------------------------------------
+C
+ double precision function dist(i1,i2)
+c
+c Calculates the distance between atoms (i1) and (i2).
+c
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.GEO'
+ include 'COMMON.CHAIN'
+ x12=c(1,i1)-c(1,i2)
+ y12=c(2,i1)-c(2,i2)
+ z12=c(3,i1)-c(3,i2)
+ dist=dsqrt(x12*x12+y12*y12+z12*z12)
+ return
+ end
+C
--- /dev/null
+ subroutine make_ensembles(islice,*)
+! construct the conformational ensembles at REMD temperatures
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ include "COMMON.MPI"
+ integer ierror,errcode,status(MPI_STATUS_SIZE)
+#endif
+ include "COMMON.IOUNITS"
+ include "COMMON.CONTROL"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.FFIELD"
+ include "COMMON.INTERACT"
+ include "COMMON.SBRIDGE"
+ include "COMMON.CHAIN"
+ include "COMMON.PROTFILES"
+ include "COMMON.PROT"
+ real*4 csingle(3,maxres2)
+ double precision fT(6),fTprim(6),fTbis(6),quot,quotl1,quotl,kfacl,
+ & eprim,ebis,temper,kfac/2.4d0/,T0/300.0d0/
+ double precision etot,evdw,evdw_t,evdw2,ees,evdw1,ebe,etors,
+ & escloc,
+ & ehpb,ecorr,ecorr5,ecorr6,eello_turn4,eello_turn3,
+ & eturn6,eel_loc,edihcnstr,etors_d,estr,evdw2_14,esccor,tt
+ integer i,ii,ik,iproc,iscor,j,k,l,ib,iparm,iprot,nlist
+ double precision qfree,sumprob,eini,efree,rmsdev
+ character*80 bxname
+ character*2 licz1,licz2
+ character*3 licz3,licz4
+ character*5 ctemper
+ integer ilen
+ external ilen
+ real*4 Fdimless(MaxStr)
+ double precision enepot(MaxStr)
+ integer iperm(MaxStr)
+ integer islice
+
+#ifdef MPI
+ if (me.eq.Master) then
+#endif
+ write (licz2,'(bz,i2.2)') islice
+ if (nslice.eq.1) then
+ if (.not.separate_parset) then
+ bxname = prefix(:ilen(prefix))//".bx"
+ else
+ write (licz3,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//"_par"//licz3//".bx"
+ endif
+ else
+ if (.not.separate_parset) then
+ bxname = prefix(:ilen(prefix))//"_slice_"//licz2//".bx"
+ else
+ write (licz3,'(bz,i3.3)') myparm
+ bxname = prefix(:ilen(prefix))//"par_"//licz3//
+ & "_slice_"//licz2//".bx"
+ endif
+ endif
+ open (ientout,file=bxname,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec1)
+#ifdef MPI
+ endif
+#endif
+ do iparm=1,nParmSet
+ if (iparm.ne.iparmprint) exit
+ call restore_parm(iparm)
+ do ib=1,nT_h(iparm)
+#ifdef DEBUG
+ write (iout,*) "iparm",iparm," ib",ib
+#endif
+ temper=1.0d0/(beta_h(ib,iparm)*1.987D-3)
+c quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+c quotl=1.0d0
+c kfacl=1.0d0
+c do l=1,5
+c quotl1=quotl
+c quotl=quotl*quot
+c kfacl=kfacl*kfac
+c fT(l)=kfacl/(kfacl-1.0d0+quotl)
+c enddo
+ if (rescale_mode.eq.1) then
+ quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+#if defined(FUNCTH)
+ tt=1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=quot
+#else
+ ft(6)=1.0d0
+#endif
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ fT(l)=kfacl/(kfacl-1.0d0+quotl)
+ enddo
+ else if (rescale_mode.eq.2) then
+ quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+#if defined(FUNCTH)
+ tt=1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/3200.d0
+#elif defined(FUNCT)
+ ft(6)=quot
+#else
+ ft(6)=1.0d0
+#endif
+ quotl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ fT(l)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
+ else if (rescale_mode.eq.0) then
+ do l=1,5
+ fT(l)=0.0d0
+ enddo
+ else
+ write (iout,*)
+ & "Error in MAKE_ENSEMBLE: Wrong RESCALE_MODE:",rescale_mode
+ call flush(iout)
+ return1
+ endif
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+ evdw=enetb(1,i,iparm)
+ evdw_t=enetb(21,i,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,i,iparm)
+ evdw2=enetb(2,i,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,i,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,i,iparm)
+ evdw1=enetb(16,i,iparm)
+#else
+ ees=enetb(3,i,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,i,iparm)
+ ecorr5=enetb(5,i,iparm)
+ ecorr6=enetb(6,i,iparm)
+ eel_loc=enetb(7,i,iparm)
+ eello_turn3=enetb(8,i,iparm)
+ eello_turn4=enetb(9,i,iparm)
+ eturn6=enetb(10,i,iparm)
+ ebe=enetb(11,i,iparm)
+ escloc=enetb(12,i,iparm)
+ etors=enetb(13,i,iparm)
+ etors_d=enetb(14,i,iparm)
+ ehpb=enetb(15,i,iparm)
+ estr=enetb(18,i,iparm)
+ esccor=enetb(19,i,iparm)
+ edihcnstr=enetb(20,i,iparm)
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#endif
+#ifdef MPI
+ Fdimless(i)=
+ & beta_h(ib,iparm)*etot-entfac(i)
+ potE(i,iparm)=etot
+#ifdef DEBUG
+ write (iout,*) i,indstart(me)+i-1,ib,
+ & 1.0d0/(1.987d-3*beta_h(ib,iparm)),potE(i,iparm),
+ & -entfac(i),Fdimless(i)
+#endif
+#else
+ Fdimless(i)=beta_h(ib,iparm)*etot-entfac(i)
+ potE(i,iparm)=etot
+#endif
+ enddo ! i
+#ifdef MPI
+ call MPI_Gatherv(Fdimless(1),scount(me),
+ & MPI_REAL,Fdimless(1),
+ & scount(0),idispl(0),MPI_REAL,Master,
+ & WHAM_COMM, IERROR)
+#ifdef DEBUG
+ call MPI_Gatherv(potE(1,iparm),scount(me),
+ & MPI_DOUBLE_PRECISION,potE(1,iparm),
+ & scount(0),idispl(0),MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM, IERROR)
+ call MPI_Gatherv(entfac(1),scount(me),
+ & MPI_DOUBLE_PRECISION,entfac(1),
+ & scount(0),idispl(0),MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM, IERROR)
+#endif
+ if (me.eq.Master) then
+#ifdef DEBUG
+ write (iout,*) "The FDIMLESS array before sorting"
+ do i=1,ntot(islice)
+ write (iout,*) i,fdimless(i)
+ enddo
+#endif
+#endif
+ do i=1,ntot(islice)
+ iperm(i)=i
+ enddo
+ call mysort1(ntot(islice),Fdimless,iperm)
+#ifdef DEBUG
+ write (iout,*) "The FDIMLESS array after sorting"
+ do i=1,ntot(islice)
+ write (iout,*) i,iperm(i),fdimless(i)
+ enddo
+#endif
+ qfree=0.0d0
+ do i=1,ntot(islice)
+ qfree=qfree+exp(-fdimless(i)+fdimless(1))
+ enddo
+c write (iout,*) "qfree",qfree
+ nlist=1
+ sumprob=0.0
+ do i=1,min0(ntot(islice),ensembles)
+ sumprob=sumprob+exp(-fdimless(i)+fdimless(1))/qfree
+#ifdef DEBUG
+ write (iout,*) i,ib,beta_h(ib,iparm),
+ & 1.0d0/(1.987d-3*beta_h(ib,iparm)),iperm(i),
+ & potE(iperm(i),iparm),
+ & -entfac(iperm(i)),fdimless(i),sumprob
+#endif
+ if (sumprob.gt.0.99d0) goto 122
+ nlist=nlist+1
+ enddo
+ 122 continue
+#ifdef MPI
+ endif
+ call MPI_Bcast(nlist, 1, MPI_INTEGER, Master, WHAM_COMM,
+ & IERROR)
+ call MPI_Bcast(iperm,nlist,MPI_INTEGER,Master,WHAM_COMM,
+ & IERROR)
+ do i=1,nlist
+ ii=iperm(i)
+ iproc=0
+ do while (ii.lt.indstart(iproc).or.ii.gt.indend(iproc))
+ iproc=iproc+1
+ enddo
+ if (iproc.ge.nprocs) then
+ write (iout,*) "Fatal error: processor out of range",iproc
+ call flush(iout)
+ if (bxfile) then
+ close (ientout)
+ else
+ close (ientout,status="delete")
+ endif
+ return1
+ endif
+ ik=ii-indstart(iproc)+1
+ if (iproc.ne.Master) then
+ if (me.eq.iproc) then
+#ifdef DEBUG
+ write (iout,*) "i",i," ii",ii," iproc",iproc," ik",ik,
+ & " energy",potE(ik,iparm)
+#endif
+ call MPI_Send(potE(ik,iparm),1,MPI_DOUBLE_PRECISION,
+ & Master,i,WHAM_COMM,IERROR)
+ else if (me.eq.Master) then
+ call MPI_Recv(enepot(i),1,MPI_DOUBLE_PRECISION,iproc,i,
+ & WHAM_COMM,STATUS,IERROR)
+ endif
+ else if (me.eq.Master) then
+ enepot(i)=potE(ik,iparm)
+ endif
+ enddo
+#else
+ do i=1,nlist
+ enepot(i)=potE(iperm(i),iparm)
+ enddo
+#endif
+#ifdef MPI
+ if (me.eq.Master) then
+#endif
+ write(licz3,'(bz,i3.3)') iparm
+ write(licz2,'(bz,i2.2)') islice
+ if (temper.lt.100.0d0) then
+ write(ctemper,'(f3.0)') temper
+ else if (temper.lt.1000.0) then
+ write (ctemper,'(f4.0)') temper
+ else
+ write (ctemper,'(f5.0)') temper
+ endif
+ if (nparmset.eq.1) then
+ if (separate_parset) then
+ write(licz4,'(bz,i3.3)') myparm
+ pdbname=prefix(:ilen(prefix))//"_par"//licz4
+ else
+ pdbname=prefix(:ilen(prefix))
+ endif
+ else
+ pdbname=prefix(:ilen(prefix))//"_parm_"//licz3
+ endif
+ if (nslice.eq.1) then
+ pdbname=pdbname(:ilen(pdbname))//"_T_"//
+ & ctemper(:ilen(ctemper))//"pdb"
+ else
+ pdbname=pdbname(:ilen(pdbname))//"_slice_"//licz2//"_T_"//
+ & ctemper(:ilen(ctemper))//"pdb"
+ endif
+ open(ipdb,file=pdbname)
+ do i=1,nlist
+ read (ientout,rec=iperm(i))
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,iscor
+ do j=1,2*nres
+ do k=1,3
+ c(k,j)=csingle(k,j)
+ enddo
+ enddo
+ eini=fdimless(i)
+ call pdbout(iperm(i),temper,eini,enepot(i),efree,rmsdev)
+ enddo
+#ifdef MPI
+ endif
+#endif
+ enddo ! ib
+ enddo ! iparm
+ if (bxfile) then
+ close(ientout)
+ else
+ close(ientout,status="delete")
+ endif
+ return
+ end
+!--------------------------------------------------
+ subroutine mysort1(n, x, ipermut)
+ implicit none
+ integer i,j,imax,ipm,n
+ real x(n)
+ integer ipermut(n)
+ real xtemp
+ do i=1,n
+ xtemp=x(i)
+ imax=i
+ do j=i+1,n
+ if (x(j).lt.xtemp) then
+ imax=j
+ xtemp=x(j)
+ endif
+ enddo
+ x(imax)=x(i)
+ x(i)=xtemp
+ ipm=ipermut(imax)
+ ipermut(imax)=ipermut(i)
+ ipermut(i)=ipm
+ enddo
+ return
+ end
--- /dev/null
+ subroutine match_contact(ishif1,ishif2,nc_match,nc_match1_max,
+ & ncont_ref,icont_ref,ncont,icont,jfrag,n_shif1,n_shif2,
+ & nc_frac,nc_req_set,istr,llocal,lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ integer ncont_ref,icont_ref(2,maxcont),ncont,icont(2,maxcont),
+ & ishift,ishif2,nc_match
+ double precision nc_frac
+ logical llocal,lprn
+ nc_match_max=0
+ do i=1,ncont_ref
+ nc_match_max=nc_match_max+
+ & min0(icont_ref(2,i)-icont_ref(1,i)-1,3)
+ enddo
+ if (istr.eq.3) then
+ nc_req=0
+ else if (nc_req_set.eq.0) then
+ nc_req=nc_match_max*nc_frac
+ else
+ nc_req = dmin1(nc_match_max*nc_frac+0.5d0,
+ & dfloat(nc_req_set)+1.0d-7)
+ endif
+c write (iout,*) "match_contact: nc_req:",nc_req
+c write (iout,*) "nc_match_max",nc_match_max
+c write (iout,*) "jfrag",jfrag," n_shif1",n_shif1,
+c & " n_shif2",n_shif2
+C Match current contact map against reference contact map; exit, if at least
+C half of the contacts match
+ call ncont_match(nc_match,nc_match1,0,0,ncont_ref,icont_ref,
+ & ncont,icont,jfrag,llocal,lprn)
+ nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",0,0," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or.
+ & nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=0
+ ishif2=0
+ return
+ endif
+C If sufficient matches are not found, try to shift contact maps up to three
+C positions.
+ if (n_shif1.gt.0) then
+ do is=1,n_shif1
+C The following four tries help to find shifted beta-sheet patterns
+C Shift "left" strand backward
+ call ncont_match(nc_match,nc_match1,-is,0,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",-is,0," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or.
+ & nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=-is
+ ishif2=0
+ return
+ endif
+C Shift "left" strand forward
+ call ncont_match(nc_match,nc_match1,is,0,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",is,0," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_req.gt.0 .and. nc_match.ge.nc_req .or.
+ & nc_req.eq.0 .and. nc_match.eq.1) then
+ ishif1=is
+ ishif2=0
+ return
+ endif
+ enddo
+ if (nc_req.eq.0) return
+C Shift "right" strand backward
+ do is=1,n_shif1
+ call ncont_match(nc_match,nc_match1,0,-is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",0,-is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=0
+ ishif2=-is
+ return
+ endif
+C Shift "right" strand upward
+ call ncont_match(nc_match,nc_match1,0,is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",0,is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=0
+ ishif2=is
+ return
+ endif
+ enddo ! is
+C Now try to shift both residues in contacts.
+ do is=1,n_shif1
+ do js=1,is
+ if (js.ne.is) then
+ call ncont_match(nc_match,nc_match1,-is,-js,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",-is,-js," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=-js
+ return
+ endif
+ call ncont_match(nc_match,nc_match1,is,js,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",is,js," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=is
+ ishif2=js
+ return
+ endif
+c
+ call ncont_match(nc_match,nc_match1,-js,-is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",-js,-is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-js
+ ishif2=-is
+ return
+ endif
+c
+ call ncont_match(nc_match,nc_match1,js,is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",js,is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=js
+ ishif2=is
+ return
+ endif
+ endif
+c
+ if (is+js.le.n_shif1) then
+ call ncont_match(nc_match,nc_match1,-is,js,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",-is,js," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=js
+ return
+ endif
+c
+ call ncont_match(nc_match,nc_match1,js,-is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",js,-is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=js
+ ishif2=-is
+ return
+ endif
+ endif
+c
+ enddo !js
+ enddo !is
+ endif
+
+ if (n_shif2.gt.0) then
+ do is=1,n_shif2
+ call ncont_match(nc_match,nc_match1,-is,-is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",-is,-is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=-is
+ ishif2=-is
+ return
+ endif
+ call ncont_match(nc_match,nc_match1,is,is,ncont_ref,
+ & icont_ref,ncont,icont,jfrag,llocal,lprn)
+ if (nc_match1.gt.nc_match1_max) nc_match1_max=nc_match1
+ if (lprn .and. nc_match.gt.0) write (iout,*)
+ & "Shift:",is,is," nc_match1",nc_match1,
+ & " nc_match=",nc_match," req'd",nc_req
+ if (nc_match.ge.nc_req) then
+ ishif1=is
+ ishif2=is
+ return
+ endif
+ enddo
+ endif
+C If this point is reached, the contact maps are different.
+ nc_match=0
+ ishif1=0
+ ishif2=0
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine ncont_match(nc_match,nc_match1,ishif1,ishif2,
+ & ncont_ref,icont_ref,ncont,icont,jfrag,llocal,lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.COMPAR'
+ logical llocal,lprn
+ integer ncont_ref,icont_ref(2,maxcont),ncont,icont(2,maxcont),
+ & icont_match(2,maxcont),ishift,ishif2,nang_pair,
+ & iang_pair(2,maxres)
+C Compare the contact map against the reference contact map; they're stored
+C in ICONT and ICONT_REF, respectively. The current contact map can be shifted.
+ if (lprn) write (iout,'(80(1h*))')
+ nc_match=0
+ nc_match1=0
+c Check the local structure by comparing dihedral angles.
+c write (iout,*) "ncont_match: ncont_ref",ncont_ref," llocal",llocal
+ if (llocal .and. ncont_ref.eq.0) then
+c If there are no contacts just compare the dihedral angles and exit.
+ call angnorm(jfrag,ishif1,ishif2,ang_cut1(jfrag),diffang,fract,
+ & lprn)
+ if (lprn) write (iout,*) "diffang:",diffang*rad2deg,
+ & " ang_cut:",ang_cut(jfrag)*rad2deg," fract",fract
+ if (diffang.le.ang_cut(jfrag) .and. fract.ge.frac_min(jfrag))
+ & then
+ nc_match=1
+ else
+ nc_match=0
+ endif
+ return
+ endif
+ nang_pair=0
+ do i=1,ncont
+ ic1=icont(1,i)+ishif1
+ ic2=icont(2,i)+ishif2
+c write (iout,*) "i",i," ic1",ic1," ic2",ic2
+ if (ic1.lt.nnt .or. ic2.gt.nct) goto 10
+ do j=1,ncont_ref
+ if (ic1.eq.icont_ref(1,j).and.ic2.eq.icont_ref(2,j)) then
+ nc_match=nc_match+min0(icont_ref(2,j)-icont_ref(1,j)-1,3)
+ nc_match1=nc_match1+1
+ icont_match(1,nc_match1)=ic1
+ icont_match(2,nc_match1)=ic2
+c call add_angpair(icont(1,i),icont_ref(1,j),
+c & nang_pair,iang_pair)
+c call add_angpair(icont(2,i),icont_ref(2,j),
+c & nang_pair,iang_pair)
+ if (lprn) write (iout,*) "Contacts:",icont(1,i),icont(2,i),
+ & " match",icont_ref(1,j),icont_ref(2,j),
+ & " shifts",ishif1,ishif2
+ goto 10
+ endif
+ enddo
+ 10 continue
+ enddo
+ if (lprn) then
+ write (iout,*) "nc_match",nc_match," nc_match1",nc_match1
+ write (iout,*) "icont_match"
+ do i=1,nc_match1
+ write (iout,*) icont_match(1,i),icont_match(2,i)
+ enddo
+ endif
+ if (llocal .and. nc_match.gt.0) then
+ call angnorm2(jfrag,ishif1,ishif2,nc_match1,icont_match,lprn,
+ & ang_cut1(jfrag),diffang,fract)
+ if (lprn) write (iout,*) "diffang:",diffang*rad2deg,
+ & " ang_cut:",ang_cut(jfrag)*rad2deg,
+ & " ang_cut1",ang_cut1(jfrag)*rad2deg
+ if (diffang.gt.ang_cut(jfrag)
+ & .or. fract.lt.frac_min(jfrag)) nc_match=0
+ endif
+c if (nc_match.gt.0) then
+c diffang = angnorm1(nang_pair,iang_pair,lprn)
+c if (diffang.gt.ang_cut(jfrag)) nc_match=0
+c endif
+ if (lprn) write (iout,*) "ishif1",ishif1," ishif2",ishif2,
+ & " diffang",rad2deg*diffang," nc_match",nc_match
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine match_secondary(jfrag,isecstr,nsec_match,lprn)
+c This subroutine compares the secondary structure (isecstr) of fragment jfrag
+c conformation considered to that of the reference conformation.
+c Returns the number of equivalent residues (nsec_match).
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.PEPTCONT'
+ include 'COMMON.COMPAR'
+ logical lprn
+ integer isecstr(maxres)
+ npart = npiece(jfrag,1)
+ nsec_match=0
+ if (lprn) then
+ write (iout,*) "match_secondary jfrag",jfrag," ifrag",
+ & (ifrag(1,i,jfrag),ifrag(2,i,jfrag),i=1,npart)
+ write (iout,'(80i1)') (isec_ref(j),j=1,nres)
+ write (iout,'(80i1)') (isecstr(j),j=1,nres)
+ endif
+ do i=1,npart
+ do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+c The residue has equivalent conformational state to that of the reference
+c structure, if:
+c a) the conformational states are equal or
+c b) the reference state is a coil and that of the conformation considered
+c is a strand or
+c c) the conformational state of the conformation considered is a strand
+c and that of the reference conformation is a coil.
+c 10/28/02 - case (b) deleted.
+ if (isecstr(j).eq.isec_ref(j) .or.
+c & isecstr(j).eq.0 .and. isec_ref(j).eq.1 .or.
+ & isec_ref(j).eq.0 .and. isecstr(j).eq.1)
+ & nsec_match=nsec_match+1
+ enddo
+ enddo
+ return
+ end
--- /dev/null
+ SUBROUTINE MATMULT(A1,A2,A3)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ DIMENSION A1(3,3),A2(3,3),A3(3,3)
+ DIMENSION AI3(3,3)
+ DO 1 I=1,3
+ DO 2 J=1,3
+ A3IJ=0.0
+ DO 3 K=1,3
+ 3 A3IJ=A3IJ+A1(I,K)*A2(K,J)
+ AI3(I,J)=A3IJ
+ 2 CONTINUE
+ 1 CONTINUE
+ DO 4 I=1,3
+ DO 4 J=1,3
+ 4 A3(I,J)=AI3(I,J)
+ RETURN
+ END
--- /dev/null
+C $Date: 1994/10/12 17:24:21 $
+C $Revision: 2.5 $
+C
+C
+C
+ logical function find_arg(ipos,line,errflag)
+ parameter (maxlen=80)
+ character*80 line
+ character*1 empty /' '/,equal /'='/
+ logical errflag
+* This function returns .TRUE., if an argument follows keyword keywd; if so
+* IPOS will point to the first non-blank character of the argument. Returns
+* .FALSE., if no argument follows the keyword; in this case IPOS points
+* to the first non-blank character of the next keyword.
+ do while (line(ipos:ipos) .eq. empty .and. ipos.le.maxlen)
+ ipos=ipos+1
+ enddo
+ errflag=.false.
+ if (line(ipos:ipos).eq.equal) then
+ find_arg=.true.
+ ipos=ipos+1
+ do while (line(ipos:ipos) .eq. empty .and. ipos.le.maxlen)
+ ipos=ipos+1
+ enddo
+ if (ipos.gt.maxlen) errflag=.true.
+ else
+ find_arg=.false.
+ endif
+ return
+ end
+ logical function find_group(iunit,jout,key1)
+ character*(*) key1
+ character*80 karta,ucase
+ integer ilen
+ external ilen
+ logical lcom
+ rewind (iunit)
+ karta=' '
+ ll=ilen(key1)
+ do while (index(ucase(karta),key1(1:ll)).eq.0.or.lcom(1,karta))
+ read (iunit,'(a)',end=10) karta
+ enddo
+ write (jout,'(2a)') '> ',karta(1:78)
+ find_group=.true.
+ return
+ 10 find_group=.false.
+ return
+ end
+ logical function iblnk(charc)
+ character*1 charc
+ integer n
+ n = ichar(charc)
+ iblnk = (n.eq.9) .or. (n.eq.10) .or. (charc.eq. ' ')
+ return
+ end
+ integer function ilen(string)
+ character*(*) string
+ logical iblnk
+
+ ilen = len(string)
+1 if ( ilen .gt. 0 ) then
+ if ( iblnk( string(ilen:ilen) ) ) then
+ ilen = ilen - 1
+ goto 1
+ endif
+ endif
+ return
+ end
+ integer function in_keywd_set(nkey,ikey,narg,keywd,keywdset)
+ character*16 keywd,keywdset(1:nkey,0:nkey)
+ character*16 ucase
+ do i=1,narg
+ if (ucase(keywd).eq.keywdset(i,ikey)) then
+* Match found
+ in_keywd_set=i
+ return
+ endif
+ enddo
+* No match to the allowed set of keywords if this point is reached.
+ in_keywd_set=0
+ return
+ end
+ character*(*) function lcase(string)
+ integer i, k, idiff
+ character*(*) string
+ character*1 c
+ character*40 chtmp
+c
+ i = len(lcase)
+ k = len(string)
+ if (i .lt. k) then
+ k = i
+ if (string(k+1:) .ne. ' ') then
+ chtmp = string
+ endif
+ endif
+ idiff = ichar('a') - ichar('A')
+ lcase = string
+ do 99 i = 1, k
+ c = string(i:i)
+ if (lge(c,'A') .and. lle(c,'Z')) then
+ lcase(i:i) = char(ichar(c) + idiff)
+ endif
+ 99 continue
+ return
+ end
+ logical function lcom(ipos,karta)
+ character*80 karta
+ character koment(2) /'!','#'/
+ lcom=.false.
+ do i=1,2
+ if (karta(ipos:ipos).eq.koment(i)) lcom=.true.
+ enddo
+ return
+ end
+ logical function lower_case(ch)
+ character*(*) ch
+ lower_case=(ch.ge.'a' .and. ch.le.'z')
+ return
+ end
+ subroutine mykey(line,keywd,ipos,blankline,errflag)
+* This subroutine seeks a non-empty substring keywd in the string LINE.
+* The substring begins with the first character different from blank and
+* "=" encountered right to the pointer IPOS (inclusively) and terminates
+* at the character left to the first blank or "=". When the subroutine is
+* exited, the pointer IPOS is moved to the position of the terminator in LINE.
+* The logical variable BLANKLINE is set at .TRUE., if LINE(IPOS:) contains
+* only separators or the maximum length of the data line (80) has been reached.
+* The logical variable ERRFLAG is set at .TRUE. if the string
+* consists only from a "=".
+ parameter (maxlen=80)
+ character*1 empty /' '/,equal /'='/,comma /','/
+ character*(*) keywd
+ character*80 line
+ logical blankline,errflag,lcom
+ errflag=.false.
+ do while (line(ipos:ipos).eq.empty .and. (ipos.le.maxlen))
+ ipos=ipos+1
+ enddo
+ if (ipos.gt.maxlen .or. lcom(ipos,line) ) then
+* At this point the rest of the input line turned out to contain only blanks
+* or to be commented out.
+ blankline=.true.
+ return
+ endif
+ blankline=.false.
+ istart=ipos
+* Checks whether the current char is a separator.
+ do while (line(ipos:ipos).ne.empty .and. line(ipos:ipos).ne.equal
+ & .and. line(ipos:ipos).ne.comma .and. ipos.le.maxlen)
+ ipos=ipos+1
+ enddo
+ iend=ipos-1
+* Error flag set to .true., if the length of the keyword was found less than 1.
+ if (iend.lt.istart) then
+ errflag=.true.
+ return
+ endif
+ keywd=line(istart:iend)
+ return
+ end
+ subroutine numstr(inum,numm)
+ character*10 huj /'0123456789'/
+ character*(*) numm
+ inumm=inum
+ inum1=inumm/10
+ inum2=inumm-10*inum1
+ inumm=inum1
+ numm(3:3)=huj(inum2+1:inum2+1)
+ inum1=inumm/10
+ inum2=inumm-10*inum1
+ inumm=inum1
+ numm(2:2)=huj(inum2+1:inum2+1)
+ inum1=inumm/10
+ inum2=inumm-10*inum1
+ inumm=inum1
+ numm(1:1)=huj(inum2+1:inum2+1)
+ return
+ end
+ character*(*) function ucase(string)
+ integer i, k, idiff
+ character*(*) string
+ character*1 c
+ character*40 chtmp
+c
+ i = len(ucase)
+ k = len(string)
+ if (i .lt. k) then
+ k = i
+ if (string(k+1:) .ne. ' ') then
+ chtmp = string
+ endif
+ endif
+ idiff = ichar('a') - ichar('A')
+ ucase = string
+ do 99 i = 1, k
+ c = string(i:i)
+ if (lge(c,'a') .and. lle(c,'z')) then
+ ucase(i:i) = char(ichar(c) - idiff)
+ endif
+ 99 continue
+ return
+ end
--- /dev/null
+ subroutine molread(*)
+C
+C Read molecular data.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.NAMES'
+ include 'COMMON.CHAIN'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ character*4 sequence(maxres)
+ integer rescode
+ double precision x(maxvar)
+ character*320 controlcard,ucase
+ dimension itype_pdb(maxres)
+ logical seq_comp
+ call card_concat(controlcard,.true.)
+ call reada(controlcard,'SCAL14',scal14,0.4d0)
+ call reada(controlcard,'SCALSCP',scalscp,1.0d0)
+ call reada(controlcard,'CUTOFF',cutoff_corr,7.0d0)
+ call reada(controlcard,'DELT_CORR',delt_corr,0.5d0)
+ r0_corr=cutoff_corr-delt_corr
+ call readi(controlcard,"NRES",nres,0)
+ iscode=index(controlcard,"ONE_LETTER")
+ if (nres.le.0) then
+ write (iout,*) "Error: no residues in molecule"
+ return1
+ endif
+ if (nres.gt.maxres) then
+ write (iout,*) "Error: too many residues",nres,maxres
+ endif
+ write(iout,*) 'nres=',nres
+C Read sequence of the protein
+ if (iscode.gt.0) then
+ read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
+ else
+ read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
+ endif
+C Convert sequence to numeric code
+ do i=1,nres
+ itype(i)=rescode(i,sequence(i),iscode)
+ enddo
+ write (iout,*) "Numeric code:"
+ write (iout,'(20i4)') (itype(i),i=1,nres)
+ do i=1,nres-1
+#ifdef PROCOR
+ if (itype(i).eq.21 .or. itype(i+1).eq.21) then
+#else
+ if (itype(i).eq.21) then
+#endif
+ itel(i)=0
+#ifdef PROCOR
+ else if (itype(i+1).ne.20) then
+#else
+ else if (itype(i).ne.20) then
+#endif
+ itel(i)=1
+ else
+ itel(i)=2
+ endif
+ enddo
+ call read_bridge
+
+ if (with_dihed_constr) then
+
+ read (inp,*) ndih_constr
+ if (ndih_constr.gt.0) then
+ read (inp,*) ftors
+ write (iout,*) 'FTORS',ftors
+ read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
+ write (iout,*)
+ & 'There are',ndih_constr,' constraints on phi angles.'
+ do i=1,ndih_constr
+ write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
+ enddo
+ do i=1,ndih_constr
+ phi0(i)=deg2rad*phi0(i)
+ drange(i)=deg2rad*drange(i)
+ enddo
+ endif
+
+ endif
+
+ nnt=1
+ nct=nres
+ if (itype(1).eq.21) nnt=2
+ if (itype(nres).eq.21) nct=nct-1
+ write(iout,*) 'NNT=',NNT,' NCT=',NCT
+c Read distance restraints
+ if (constr_dist.gt.0) then
+ if (refstr) call read_ref_structure(*11)
+ call read_dist_constr
+ call hpb_partition
+ endif
+
+ call setup_var
+ call init_int_table
+ if (ns.gt.0) then
+ write (iout,'(/a,i3,a)') 'The chain contains',ns,
+ & ' disulfide-bridging cysteines.'
+ write (iout,'(20i4)') (iss(i),i=1,ns)
+ write (iout,'(/a/)') 'Pre-formed links are:'
+ do i=1,nss
+ i1=ihpb(i)-nres
+ i2=jhpb(i)-nres
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(2a,i3,3a,i3,a,3f10.3)')
+ & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',
+ & dhpb(i),ebr,forcon(i)
+ enddo
+ endif
+ write (iout,'(a)')
+ return
+ 11 stop "Error reading reference structure"
+ end
+c-----------------------------------------------------------------------------
+ logical function seq_comp(itypea,itypeb,length)
+ implicit none
+ integer length,itypea(length),itypeb(length)
+ integer i
+ do i=1,length
+ if (itypea(i).ne.itypeb(i)) then
+ seq_comp=.false.
+ return
+ endif
+ enddo
+ seq_comp=.true.
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine read_bridge
+C Read information about disulfide bridges.
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ include 'COMMON.CHAIN'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+C Read bridging residues.
+ read (inp,*) ns,(iss(i),i=1,ns)
+ print *,'ns=',ns
+ write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
+C Check whether the specified bridging residues are cystines.
+ do i=1,ns
+ if (itype(iss(i)).ne.1) then
+ write (iout,'(2a,i3,a)')
+ & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & ' can form a disulfide bridge?!!!'
+ write (*,'(2a,i3,a)')
+ & 'Do you REALLY think that the residue ',restyp(iss(i)),i,
+ & ' can form a disulfide bridge?!!!'
+ stop
+ endif
+ enddo
+C Read preformed bridges.
+ if (ns.gt.0) then
+ read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
+ write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
+ if (nss.gt.0) then
+ nhpb=nss
+C Check if the residues involved in bridges are in the specified list of
+C bridging residues.
+ do i=1,nss
+ do j=1,i-1
+ if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
+ & .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
+ write (iout,'(a,i3,a)') 'Disulfide pair',i,
+ & ' contains residues present in other pairs.'
+ write (*,'(a,i3,a)') 'Disulfide pair',i,
+ & ' contains residues present in other pairs.'
+ stop
+ endif
+ enddo
+ do j=1,ns
+ if (ihpb(i).eq.iss(j)) goto 10
+ enddo
+ write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
+ 10 continue
+ do j=1,ns
+ if (jhpb(i).eq.iss(j)) goto 20
+ enddo
+ write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
+ 20 continue
+ dhpb(i)=dbr
+ forcon(i)=fbr
+ enddo
+ do i=1,nss
+ ihpb(i)=ihpb(i)+nres
+ jhpb(i)=jhpb(i)+nres
+ enddo
+ endif
+ endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine read_angles(kanal,iscor,energ,iprot,*)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ character*80 lineh
+ read(kanal,'(a80)',end=10,err=10) lineh
+ read(lineh(:5),*,err=8) ic
+ read(lineh(6:),*,err=8) energ
+ goto 9
+ 8 ic=1
+ print *,'error, assuming e=1d10',lineh
+ energ=1d10
+ nss=0
+ 9 continue
+ read(lineh(18:),*,end=10,err=10) nss
+ IF (NSS.LT.9) THEN
+ read (lineh(20:),*,end=10,err=10)
+ & (IHPB(I),JHPB(I),I=1,NSS),iscor
+ ELSE
+ read (lineh(20:),*,end=10,err=10) (IHPB(I),JHPB(I),I=1,8)
+ read (kanal,*,end=10,err=10) (IHPB(I),JHPB(I),
+ & I=9,NSS),iscor
+ ENDIF
+c print *,"energy",energ," iscor",iscor
+ read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
+ read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
+ read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
+ read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
+ do i=1,nres
+ theta(i)=deg2rad*theta(i)
+ phi(i)=deg2rad*phi(i)
+ alph(i)=deg2rad*alph(i)
+ omeg(i)=deg2rad*omeg(i)
+ enddo
+ return
+ 10 return1
+ end
+c-------------------------------------------------------------------------------
+ subroutine read_dist_constr
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SBRIDGE'
+ integer ifrag_(2,100),ipair_(2,100)
+ double precision wfrag_(100),wpair_(100)
+ character*500 controlcard
+c write (iout,*) "Calling read_dist_constr"
+c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
+c call flush(iout)
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,"NFRAG",nfrag_,0)
+ call readi(controlcard,"NPAIR",npair_,0)
+ call readi(controlcard,"NDIST",ndist_,0)
+ call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
+ call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
+ call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
+ call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
+ call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
+ write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
+ write (iout,*) "IFRAG"
+ do i=1,nfrag_
+ write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
+ enddo
+ write (iout,*) "IPAIR"
+ do i=1,npair_
+ write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
+ enddo
+ call flush(iout)
+ if (.not.refstr .and. nfrag_.gt.0) then
+ write (iout,*)
+ & "ERROR: no reference structure to compute distance restraints"
+ write (iout,*)
+ & "Restraints must be specified explicitly (NDIST=number)"
+ stop
+ endif
+ if (nfrag_.lt.2 .and. npair_.gt.0) then
+ write (iout,*) "ERROR: Less than 2 fragments specified",
+ & " but distance restraints between pairs requested"
+ stop
+ endif
+ call flush(iout)
+ do i=1,nfrag_
+ if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
+ if (ifrag_(2,i).gt.nstart_sup+nsup-1)
+ & ifrag_(2,i)=nstart_sup+nsup-1
+c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
+ call flush(iout)
+ if (wfrag_(i).gt.0.0d0) then
+ do j=ifrag_(1,i),ifrag_(2,i)-1
+ do k=j+1,ifrag_(2,i)
+ write (iout,*) "j",j," k",k
+ ddjk=dist(j,k)
+ if (constr_dist.eq.1) then
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)
+ else if (constr_dist.eq.2) then
+ if (ddjk.le.dist_cut) then
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)
+ endif
+ else
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ dhpb(nhpb)=ddjk
+ forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
+ endif
+ write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+ enddo
+ enddo
+ endif
+ enddo
+ do i=1,npair_
+ if (wpair_(i).gt.0.0d0) then
+ ii = ipair_(1,i)
+ jj = ipair_(2,i)
+ if (ii.gt.jj) then
+ itemp=ii
+ ii=jj
+ jj=itemp
+ endif
+ do j=ifrag_(1,ii),ifrag_(2,ii)
+ do k=ifrag_(1,jj),ifrag_(2,jj)
+ nhpb=nhpb+1
+ ihpb(nhpb)=j
+ jhpb(nhpb)=k
+ forcon(nhpb)=wpair_(i)
+ dhpb(nhpb)=dist(j,k)
+ write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+ enddo
+ enddo
+ endif
+ enddo
+ do i=1,ndist_
+ read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+ & ibecarb(i),forcon(nhpb+1)
+ if (forcon(nhpb+1).gt.0.0d0) then
+ nhpb=nhpb+1
+ if (ibecarb(i).gt.0) then
+ ihpb(i)=ihpb(i)+nres
+ jhpb(i)=jhpb(i)+nres
+ endif
+ if (dhpb(nhpb).eq.0.0d0)
+ & dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+ endif
+ enddo
+ do i=1,nhpb
+ write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
+ & i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
+ enddo
+ call flush(iout)
+ return
+ end
--- /dev/null
+ subroutine mygetenv(string,var)
+C
+C Version 1.0
+C
+C This subroutine passes the environmental variables to FORTRAN program.
+C If the flags -DMYGETENV and -DMPI are not for compilation, it calls the
+C standard FORTRAN GETENV subroutine. If both flags are set, the subroutine
+C reads the environmental variables from $HOME/.env
+C
+C Usage: As for the standard FORTRAN GETENV subroutine.
+C
+C Purpose: some versions/installations of MPI do not transfer the environmental
+C variables to slave processors, if these variables are set in the shell script
+C from which mpirun is called.
+C
+C A.Liwo, 7/29/01
+C
+ implicit none
+ character*(*) string,var
+#if defined(MYGETENV) && defined(MPI)
+ include "DIMENSIONS.ZSCOPT"
+ include "mpif.h"
+ include "COMMON.MPI"
+ character*360 ucase
+ external ucase
+ character*360 string1(360),karta
+ character*240 home
+ integer i,n,ilen
+ external ilen
+ call getenv("HOME",home)
+ open(99,file=home(:ilen(home))//"/.env",status="OLD",err=112)
+ do while (.true.)
+ read (99,end=111,err=111,'(a)') karta
+ do i=1,80
+ string1(i)=" "
+ enddo
+ call split_string(karta,string1,80,n)
+ if (ucase(string1(1)(:ilen(string1(1)))).eq."SETENV" .and.
+ & string1(2)(:ilen(string1(2))).eq.string(:ilen(string)) ) then
+ var=string1(3)
+ print *,"Processor",me,": ",var(:ilen(var)),
+ & " assigned to ",string(:ilen(string))
+ close(99)
+ return
+ endif
+ enddo
+ 111 print *,"Environment variable ",string(:ilen(string))," not set."
+ close(99)
+ return
+ 112 print *,"Error opening environment file!"
+#else
+ call getenv(string,var)
+#endif
+ return
+ end
--- /dev/null
+ subroutine imysort(n, m, mm, x, y, z, z1, z2, z3, z4, z5, z6)
+ implicit none
+ integer n,m,mm
+ integer x(m,mm,n),y(n),z(n),z1(2,n),z6(n),xmin,xtemp
+ double precision z2(n),z3(n),z4(n),z5(n)
+ double precision xxtemp
+ integer i,j,k,imax
+ do i=1,n
+ xmin=x(1,1,i)
+ imax=i
+ do j=i+1,n
+ if (x(1,1,j).lt.xmin) then
+ imax=j
+ xmin=x(1,1,j)
+ endif
+ enddo
+ xxtemp=z2(imax)
+ z2(imax)=z2(i)
+ z2(i)=xxtemp
+ xxtemp=z3(imax)
+ z3(imax)=z3(i)
+ z3(i)=xxtemp
+ xxtemp=z4(imax)
+ z4(imax)=z4(i)
+ z4(i)=xxtemp
+ xxtemp=z5(imax)
+ z5(imax)=z5(i)
+ z5(i)=xxtemp
+ xtemp=y(imax)
+ y(imax)=y(i)
+ y(i)=xtemp
+ xtemp=z(imax)
+ z(imax)=z(i)
+ z(i)=xtemp
+ xtemp=z6(imax)
+ z6(imax)=z6(i)
+ z6(i)=xtemp
+ do j=1,2
+ xtemp=z1(j,imax)
+ z1(j,imax)=z1(j,i)
+ z1(j,i)=xtemp
+ enddo
+ do j=1,m
+ do k=1,mm
+ xtemp=x(j,k,imax)
+ x(j,k,imax)=x(j,k,i)
+ x(j,k,i)=xtemp
+ enddo
+ enddo
+ enddo
+ return
+ end
--- /dev/null
+ subroutine odlodc(r1,r2,a,b,uu,vv,aa,bb,dd)
+ implicit real*8 (a-h,o-z)
+ dimension r1(3),r2(3),a(3),b(3),x(3),y(3)
+ odl(u,v) = (r1(1)-r2(1))**2+(r1(2)-r2(2))**2+(r1(3)-r2(3))**2
+ & + 2*ar*u - 2*br*v - 2*ab*u*v + aa*u**2 + bb*v**2
+c print *,"r1",(r1(i),i=1,3)
+c print *,"r2",(r2(i),i=1,3)
+c print *,"a",(a(i),i=1,3)
+c print *,"b",(b(i),i=1,3)
+ aa = a(1)**2+a(2)**2+a(3)**2
+ bb = b(1)**2+b(2)**2+b(3)**2
+ ab = a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
+ ar = a(1)*(r1(1)-r2(1))+a(2)*(r1(2)-r2(2))+a(3)*(r1(3)-r2(3))
+ br = b(1)*(r1(1)-r2(1))+b(2)*(r1(2)-r2(2))+b(3)*(r1(3)-r2(3))
+ det = aa*bb-ab**2
+c print *,'aa',aa,' bb',bb,' ab',ab,' ar',ar,' br',br,' det',det
+ uu = (-ar*bb+br*ab)/det
+ vv = (br*aa-ar*ab)/det
+c print *,u,v
+ uu=dmin1(uu,1.0d0)
+ uu=dmax1(uu,0.0d0)
+ vv=dmin1(vv,1.0d0)
+ vv=dmax1(vv,0.0d0)
+ dd1 = odl(uu,vv)
+ dd2 = odl(0.0d0,0.0d0)
+ dd3 = odl(0.0d0,1.0d0)
+ dd4 = odl(1.0d0,0.0d0)
+ dd5 = odl(1.0d0,1.0d0)
+ dd = dsqrt(dmin1(dd1,dd2,dd3,dd4,dd5))
+ if (dd.eq.dd2) then
+ uu=0.0d0
+ vv=0.0d0
+ else if (dd.eq.dd3) then
+ uu=0.0d0
+ vv=1.0d0
+ else if (dd.eq.dd4) then
+ uu=1.0d0
+ vv=0.0d0
+ else if (dd.eq.dd5) then
+ uu=1.0d0
+ vv=1.0d0
+ endif
+c Control check
+c do i=1,3
+c x(i)=r1(i)+u*a(i)
+c y(i)=r2(i)+v*b(i)
+c enddo
+c dd1 = (x(1)-y(1))**2+(x(2)-y(2))**2+(x(3)-y(3))**2
+c dd1 = dsqrt(dd1)
+ aa = dsqrt(aa)
+ bb = dsqrt(bb)
+c write (8,*) uu,vv,dd,dd1
+c print *,dd,dd1
+ return
+ end
--- /dev/null
+ subroutine openunits
+#ifdef WIN
+ use dfport
+#endif
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+#ifdef MPI
+ include 'mpif.h'
+ include 'COMMON.MPI'
+ integer MyRank
+ character*3 liczba
+#endif
+ include 'COMMON.IOUNITS'
+ integer lenpre,lenpot,ilen
+ external ilen
+
+#ifdef MPI
+ MyRank=Me
+#endif
+ call mygetenv('PREFIX',prefix)
+ call mygetenv('SCRATCHDIR',scratchdir)
+ call mygetenv('POT',pot)
+ lenpre=ilen(prefix)
+ lenpot=ilen(pot)
+ call mygetenv('POT',pot)
+ entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
+C Get the names and open the input files
+ open (1,file=prefix(:ilen(prefix))//'.inp',status='old')
+C Get parameter filenames and open the parameter files.
+ call mygetenv('BONDPAR',bondname)
+ open (ibond,file=bondname,status='old')
+ call mygetenv('THETPAR',thetname)
+ open (ithep,file=thetname,status='old')
+ call mygetenv('ROTPAR',rotname)
+ open (irotam,file=rotname,status='old')
+ call mygetenv('TORPAR',torname)
+ open (itorp,file=torname,status='old')
+ call mygetenv('TORDPAR',tordname)
+ open (itordp,file=tordname,status='old')
+ call mygetenv('FOURIER',fouriername)
+ open (ifourier,file=fouriername,status='old')
+ call mygetenv('SCCORPAR',sccorname)
+ open (isccor,file=sccorname,status='old')
+ call mygetenv('ELEPAR',elename)
+ open (ielep,file=elename,status='old')
+ call mygetenv('SIDEPAR',sidename)
+ open (isidep,file=sidename,status='old')
+ call mygetenv('SIDEP',sidepname)
+ open (isidep1,file=sidepname,status="old")
+#ifndef OLDSCP
+C
+C 8/9/01 In the newest version SCp interaction constants are read from a file
+C Use -DOLDSCP to use hard-coded constants instead.
+C
+ call mygetenv('SCPPAR',scpname)
+ open (iscpp,file=scpname,status='old')
+#endif
+#ifdef MPL
+ if (MyID.eq.BossID) then
+ MyRank = MyID/fgProcs
+#endif
+#ifdef MPI
+ print *,'OpenUnits: processor',MyRank
+ call numstr(MyRank,liczba)
+ outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//liczba
+#else
+ outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
+#endif
+ open(iout,file=outname,status='unknown')
+ write (iout,'(80(1h-))')
+ write (iout,'(30x,a)') "FILE ASSIGNMENT"
+ write (iout,'(80(1h-))')
+ write (iout,*) "Input file : ",
+ & prefix(:ilen(prefix))//'.inp'
+ write (iout,*) "Output file : ",
+ & outname(:ilen(outname))
+ write (iout,*)
+ write (iout,*) "Sidechain potential file : ",
+ & sidename(:ilen(sidename))
+#ifndef OLDSCP
+ write (iout,*) "SCp potential file : ",
+ & scpname(:ilen(scpname))
+#endif
+ write (iout,*) "Electrostatic potential file : ",
+ & elename(:ilen(elename))
+ write (iout,*) "Cumulant coefficient file : ",
+ & fouriername(:ilen(fouriername))
+ write (iout,*) "Torsional parameter file : ",
+ & torname(:ilen(torname))
+ write (iout,*) "Double torsional parameter file : ",
+ & tordname(:ilen(tordname))
+ write (iout,*) "Backbone-rotamer parameter file : ",
+ & sccorname(:ilen(sccorname))
+ write (iout,*) "Bond & inertia constant file : ",
+ & bondname(:ilen(bondname))
+ write (iout,*) "Bending parameter file : ",
+ & thetname(:ilen(thetname))
+ write (iout,*) "Rotamer parameter file : ",
+ & rotname(:ilen(rotname))
+ write (iout,'(80(1h-))')
+ write (iout,*)
+ return
+ end
+
--- /dev/null
+ subroutine parmread(iparm,*)
+C
+C Read the parameters of the probability distributions of the virtual-bond
+C valence angles and the side chains and energy parameters.
+C
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.WEIGHTS'
+ include 'COMMON.ENEPS'
+ include 'COMMON.SCCOR'
+ include 'COMMON.SCROT'
+ include 'COMMON.FREE'
+ character*1 t1,t2,t3
+ character*1 onelett(4) /"G","A","P","D"/
+ logical lprint
+ dimension blower(3,3,maxlob)
+ character*800 controlcard
+ character*256 bondname_t,thetname_t,rotname_t,torname_t,
+ & tordname_t,fouriername_t,elename_t,sidename_t,scpname_t,
+ & sccorname_t
+ integer ilen
+ external ilen
+ character*16 key
+ integer iparm
+ double precision ip,mp
+C
+C Body
+C
+C Set LPRINT=.TRUE. for debugging
+ dwa16=2.0d0**(1.0d0/6.0d0)
+ lprint=.true.
+ itypro=20
+C Assign virtual-bond length
+ vbl=3.8D0
+ vblinv=1.0D0/vbl
+ vblinv2=vblinv*vblinv
+ call card_concat(controlcard,.true.)
+ wname(4)="WCORRH"
+ do i=1,n_ene
+ key = wname(i)(:ilen(wname(i)))
+ call reada(controlcard,key(:ilen(key)),ww(i),1.0d0)
+ enddo
+
+ write (iout,*) "iparm",iparm," myparm",myparm
+c If reading not own parameters, skip assignment
+
+ if (iparm.eq.myparm .or. .not.separate_parset) then
+
+c
+c Setup weights for UNRES
+c
+ wsc=ww(1)
+ wscp=ww(2)
+ welec=ww(3)
+ wcorr=ww(4)
+ wcorr5=ww(5)
+ wcorr6=ww(6)
+ wel_loc=ww(7)
+ wturn3=ww(8)
+ wturn4=ww(9)
+ wturn6=ww(10)
+ wang=ww(11)
+ wscloc=ww(12)
+ wtor=ww(13)
+ wtor_d=ww(14)
+ wvdwpp=ww(16)
+ wstrain=ww(15)
+ wbond=ww(18)
+ wsccor=ww(19)
+
+ endif
+
+ call card_concat(controlcard,.false.)
+
+c Return if not own parameters
+
+ if (iparm.ne.myparm .and. separate_parset) return
+
+ call reads(controlcard,"BONDPAR",bondname_t,bondname)
+ open (ibond,file=bondname_t,status='old')
+ rewind(ibond)
+ call reads(controlcard,"THETPAR",thetname_t,thetname)
+ open (ithep,file=thetname_t,status='old')
+ rewind(ithep)
+ call reads(controlcard,"ROTPAR",rotname_t,rotname)
+ open (irotam,file=rotname_t,status='old')
+ rewind(irotam)
+ call reads(controlcard,"TORPAR",torname_t,torname)
+ open (itorp,file=torname_t,status='old')
+ rewind(itorp)
+ call reads(controlcard,"TORDPAR",tordname_t,tordname)
+ open (itordp,file=tordname_t,status='old')
+ rewind(itordp)
+ call reads(controlcard,"SCCORAR",sccorname_t,sccorname)
+ open (isccor,file=sccorname_t,status='old')
+ rewind(isccor)
+ call reads(controlcard,"FOURIER",fouriername_t,fouriername)
+ open (ifourier,file=fouriername_t,status='old')
+ rewind(ifourier)
+ call reads(controlcard,"ELEPAR",elename_t,elename)
+ open (ielep,file=elename_t,status='old')
+ rewind(ielep)
+ call reads(controlcard,"SIDEPAR",sidename_t,sidename)
+ open (isidep,file=sidename_t,status='old')
+ rewind(isidep)
+ call reads(controlcard,"SCPPAR",scpname_t,scpname)
+ open (iscpp,file=scpname_t,status='old')
+ rewind(iscpp)
+ write (iout,*) "Parameter set:",iparm
+ write (iout,*) "Energy-term weights:"
+ do i=1,n_ene
+ write (iout,'(a16,f10.5)') wname(i),ww(i)
+ enddo
+ write (iout,*) "Sidechain potential file : ",
+ & sidename_t(:ilen(sidename_t))
+#ifndef OLDSCP
+ write (iout,*) "SCp potential file : ",
+ & scpname_t(:ilen(scpname_t))
+#endif
+ write (iout,*) "Electrostatic potential file : ",
+ & elename_t(:ilen(elename_t))
+ write (iout,*) "Cumulant coefficient file : ",
+ & fouriername_t(:ilen(fouriername_t))
+ write (iout,*) "Torsional parameter file : ",
+ & torname_t(:ilen(torname_t))
+ write (iout,*) "Double torsional parameter file : ",
+ & tordname_t(:ilen(tordname_t))
+ write (iout,*) "Backbone-rotamer parameter file : ",
+ & sccorname(:ilen(sccorname))
+ write (iout,*) "Bond & inertia constant file : ",
+ & bondname_t(:ilen(bondname_t))
+ write (iout,*) "Bending parameter file : ",
+ & thetname_t(:ilen(thetname_t))
+ write (iout,*) "Rotamer parameter file : ",
+ & rotname_t(:ilen(rotname_t))
+
+c
+c Read the virtual-bond parameters, masses, and moments of inertia
+c and Stokes' radii of the peptide group and side chains
+c
+#ifdef CRYST_BOND
+ read (ibond,*,end=110,err=110) vbldp0,akp
+ do i=1,ntyp
+ nbondterm(i)=1
+ read (ibond,*,end=110,err=110) vbldsc0(1,i),aksc(1,i)
+ dsc(i) = vbldsc0(1,i)
+ if (i.eq.10) then
+ dsc_inv(i)=0.0D0
+ else
+ dsc_inv(i)=1.0D0/dsc(i)
+ endif
+ enddo
+#else
+ read (ibond,*,end=110,err=110) ijunk,vbldp0,akp,rjunk
+ do i=1,ntyp
+ read (ibond,*,end=110,err=110) nbondterm(i),(vbldsc0(j,i),
+ & aksc(j,i),abond0(j,i),
+ & j=1,nbondterm(i))
+ dsc(i) = vbldsc0(1,i)
+ if (i.eq.10) then
+ dsc_inv(i)=0.0D0
+ else
+ dsc_inv(i)=1.0D0/dsc(i)
+ endif
+ enddo
+#endif
+ if (lprint) then
+ write(iout,'(/a/)')"Force constants virtual bonds:"
+ write (iout,'(a10,a3,6a10)') 'Type','N','VBL','K',
+ & 'inertia','Pstok'
+ write(iout,'(a10,i3,6f10.5)') "p",1,vbldp0,akp,0.0d0
+ do i=1,ntyp
+ write (iout,'(a10,i3,6f10.5)') restyp(i),nbondterm(i),
+ & vbldsc0(1,i),aksc(1,i),abond0(1,i)
+ do j=2,nbondterm(i)
+ write (iout,'(13x,3f10.5)')
+ & vbldsc0(j,i),aksc(j,i),abond0(j,i)
+ enddo
+ enddo
+ endif
+#ifdef CRYST_THETA
+C
+C Read the parameters of the probability distribution/energy expression
+C of the virtual-bond valence angles theta
+C
+ do i=1,ntyp
+ read (ithep,*,end=111,err=111) a0thet(i),(athet(j,i),j=1,2),
+ & (bthet(j,i),j=1,2)
+ read (ithep,*,end=111,err=111) (polthet(j,i),j=0,3)
+ read (ithep,*,end=111,err=111) (gthet(j,i),j=1,3)
+ read (ithep,*,end=111,err=111) theta0(i),sig0(i),sigc0(i)
+ sigc0(i)=sigc0(i)**2
+ enddo
+ close (ithep)
+ if (lprint) then
+c write (iout,'(a)')
+c & 'Parameters of the virtual-bond valence angles:'
+c write (iout,'(/a/9x,5a/79(1h-))') 'Fourier coefficients:',
+c & ' ATHETA0 ',' A1 ',' A2 ',
+c & ' B1 ',' B2 '
+c do i=1,ntyp
+c write(iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,
+c & a0thet(i),(athet(j,i),j=1,2),(bthet(j,i),j=1,2)
+c enddo
+c write (iout,'(/a/9x,5a/79(1h-))')
+c & 'Parameters of the expression for sigma(theta_c):',
+c & ' ALPH0 ',' ALPH1 ',' ALPH2 ',
+c & ' ALPH3 ',' SIGMA0C '
+c do i=1,ntyp
+c write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,
+c & (polthet(j,i),j=0,3),sigc0(i)
+c enddo
+c write (iout,'(/a/9x,5a/79(1h-))')
+c & 'Parameters of the second gaussian:',
+c & ' THETA0 ',' SIGMA0 ',' G1 ',
+c & ' G2 ',' G3 '
+c do i=1,ntyp
+c write (iout,'(a3,i4,2x,5(1pe14.5))') restyp(i),i,theta0(i),
+c & sig0(i),(gthet(j,i),j=1,3)
+c enddo
+ write (iout,'(a)')
+ & 'Parameters of the virtual-bond valence angles:'
+ write (iout,'(/a/9x,5a/79(1h-))')
+ & 'Coefficients of expansion',
+ & ' theta0 ',' a1*10^2 ',' a2*10^2 ',
+ & ' b1*10^1 ',' b2*10^1 '
+ do i=1,ntyp
+ write(iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),
+ & a0thet(i),(100*athet(j,i),j=1,2),(10*bthet(j,i),j=1,2)
+ enddo
+ write (iout,'(/a/9x,5a/79(1h-))')
+ & 'Parameters of the expression for sigma(theta_c):',
+ & ' alpha0 ',' alph1 ',' alph2 ',
+ & ' alhp3 ',' sigma0c '
+ do i=1,ntyp
+ write (iout,'(a3,1h&,2x,5(1pe12.3,1h&))') restyp(i),
+ & (polthet(j,i),j=0,3),sigc0(i)
+ enddo
+ write (iout,'(/a/9x,5a/79(1h-))')
+ & 'Parameters of the second gaussian:',
+ & ' theta0 ',' sigma0*10^2 ',' G1*10^-1',
+ & ' G2 ',' G3*10^1 '
+ do i=1,ntyp
+ write (iout,'(a3,1h&,2x,5(f8.3,1h&))') restyp(i),theta0(i),
+ & 100*sig0(i),gthet(1,i)*0.1D0,gthet(2,i),gthet(3,i)*10.0D0
+ enddo
+ endif
+#else
+C
+C Read the parameters of Utheta determined from ab initio surfaces
+C Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
+C
+ read (ithep,*,end=111,err=111) nthetyp,ntheterm,ntheterm2,
+ & ntheterm3,nsingle,ndouble
+ nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
+ read (ithep,*,end=111,err=111) (ithetyp(i),i=1,ntyp1)
+ do i=1,maxthetyp
+ do j=1,maxthetyp
+ do k=1,maxthetyp
+ aa0thet(i,j,k)=0.0d0
+ do l=1,ntheterm
+ aathet(l,i,j,k)=0.0d0
+ enddo
+ do l=1,ntheterm2
+ do m=1,nsingle
+ bbthet(m,l,i,j,k)=0.0d0
+ ccthet(m,l,i,j,k)=0.0d0
+ ddthet(m,l,i,j,k)=0.0d0
+ eethet(m,l,i,j,k)=0.0d0
+ enddo
+ enddo
+ do l=1,ntheterm3
+ do m=1,ndouble
+ do mm=1,ndouble
+ ffthet(mm,m,l,i,j,k)=0.0d0
+ ggthet(mm,m,l,i,j,k)=0.0d0
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ do i=1,nthetyp
+ do j=1,nthetyp
+ do k=1,nthetyp
+ read (ithep,'(3a)',end=111,err=111) res1,res2,res3
+ read (ithep,*,end=111,err=111) aa0thet(i,j,k)
+ read (ithep,*,end=111,err=111)(aathet(l,i,j,k),l=1,ntheterm)
+ read (ithep,*,end=111,err=111)
+ & ((bbthet(lll,ll,i,j,k),lll=1,nsingle),
+ & (ccthet(lll,ll,i,j,k),lll=1,nsingle),
+ & (ddthet(lll,ll,i,j,k),lll=1,nsingle),
+ & (eethet(lll,ll,i,j,k),lll=1,nsingle),ll=1,ntheterm2)
+ read (ithep,*,end=111,err=111)
+ & (((ffthet(llll,lll,ll,i,j,k),ffthet(lll,llll,ll,i,j,k),
+ & ggthet(llll,lll,ll,i,j,k),ggthet(lll,llll,ll,i,j,k),
+ & llll=1,lll-1),lll=2,ndouble),ll=1,ntheterm3)
+ enddo
+ enddo
+ enddo
+C
+C For dummy ends assign glycine-type coefficients of theta-only terms; the
+C coefficients of theta-and-gamma-dependent terms are zero.
+C
+ do i=1,nthetyp
+ do j=1,nthetyp
+ do l=1,ntheterm
+ aathet(l,i,j,nthetyp+1)=aathet(l,i,j,1)
+ aathet(l,nthetyp+1,i,j)=aathet(l,1,i,j)
+ enddo
+ aa0thet(i,j,nthetyp+1)=aa0thet(i,j,1)
+ aa0thet(nthetyp+1,i,j)=aa0thet(1,i,j)
+ enddo
+ do l=1,ntheterm
+ aathet(l,nthetyp+1,i,nthetyp+1)=aathet(l,1,i,1)
+ enddo
+ aa0thet(nthetyp+1,i,nthetyp+1)=aa0thet(1,i,1)
+ enddo
+C
+C Control printout of the coefficients of virtual-bond-angle potentials
+C
+ if (lprint) then
+ write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
+ do i=1,nthetyp+1
+ do j=1,nthetyp+1
+ do k=1,nthetyp+1
+ write (iout,'(//4a)')
+ & 'Type ',onelett(i),onelett(j),onelett(k)
+ write (iout,'(//a,10x,a)') " l","a[l]"
+ write (iout,'(i2,1pe15.5)') 0,aa0thet(i,j,k)
+ write (iout,'(i2,1pe15.5)')
+ & (l,aathet(l,i,j,k),l=1,ntheterm)
+ do l=1,ntheterm2
+ write (iout,'(//2h m,4(9x,a,3h[m,i1,1h]))')
+ & "b",l,"c",l,"d",l,"e",l
+ do m=1,nsingle
+ write (iout,'(i2,4(1pe15.5))') m,
+ & bbthet(m,l,i,j,k),ccthet(m,l,i,j,k),
+ & ddthet(m,l,i,j,k),eethet(m,l,i,j,k)
+ enddo
+ enddo
+ do l=1,ntheterm3
+ write (iout,'(//3hm,n,4(6x,a,5h[m,n,i1,1h]))')
+ & "f+",l,"f-",l,"g+",l,"g-",l
+ do m=2,ndouble
+ do n=1,m-1
+ write (iout,'(i1,1x,i1,4(1pe15.5))') n,m,
+ & ffthet(n,m,l,i,j,k),ffthet(m,n,l,i,j,k),
+ & ggthet(n,m,l,i,j,k),ggthet(m,n,l,i,j,k)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ call flush(iout)
+ endif
+#endif
+
+#ifdef CRYST_SC
+C
+C Read the parameters of the probability distribution/energy expression
+C of the side chains.
+C
+ do i=1,ntyp
+ read (irotam,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
+ if (i.eq.10) then
+ dsc_inv(i)=0.0D0
+ else
+ dsc_inv(i)=1.0D0/dsc(i)
+ endif
+ if (i.ne.10) then
+ do j=1,nlob(i)
+ do k=1,3
+ do l=1,3
+ blower(l,k,j)=0.0D0
+ enddo
+ enddo
+ enddo
+ bsc(1,i)=0.0D0
+ read(irotam,*,end=112,err=112)(censc(k,1,i),k=1,3),
+ & ((blower(k,l,1),l=1,k),k=1,3)
+ do j=2,nlob(i)
+ read (irotam,*,end=112,err=112) bsc(j,i)
+ read (irotam,*,end=112,err=112) (censc(k,j,i),k=1,3),
+ & ((blower(k,l,j),l=1,k),k=1,3)
+ enddo
+ do j=1,nlob(i)
+ do k=1,3
+ do l=1,k
+ akl=0.0D0
+ do m=1,3
+ akl=akl+blower(k,m,j)*blower(l,m,j)
+ enddo
+ gaussc(k,l,j,i)=akl
+ gaussc(l,k,j,i)=akl
+ enddo
+ enddo
+ enddo
+ endif
+ enddo
+ close (irotam)
+ if (lprint) then
+ write (iout,'(/a)') 'Parameters of side-chain local geometry'
+ do i=1,ntyp
+ nlobi=nlob(i)
+ if (nlobi.gt.0) then
+ write (iout,'(/3a,i2,a,f8.3)') 'Residue type: ',restyp(i),
+ & ' # of gaussian lobes:',nlobi,' dsc:',dsc(i)
+c write (iout,'(/a,8x,i1,4(25x,i1))') 'Lobe:',(j,j=1,nlobi)
+c write (iout,'(a,f10.4,4(16x,f10.4))')
+c & 'Center ',(bsc(j,i),j=1,nlobi)
+c write (iout,'(5(2x,3f8.4))') ((censc(k,j,i),k=1,3),j=1,nlobi)
+ write (iout,'(1h&,a,3(2h&&,f8.3,2h&&))')
+ & 'log h',(bsc(j,i),j=1,nlobi)
+ write (iout,'(1h&,a,3(1h&,f8.3,1h&,f8.3,1h&,f8.3,1h&))')
+ & 'x',((censc(k,j,i),k=1,3),j=1,nlobi)
+c write (iout,'(a)')
+c do j=1,nlobi
+c ind=0
+c do k=1,3
+c do l=1,k
+c ind=ind+1
+c blower(k,l,j)=gaussc(ind,j,i)
+c enddo
+c enddo
+c enddo
+ do k=1,3
+ write (iout,'(2h& ,5(2x,1h&,3(f7.3,1h&)))')
+ & ((gaussc(k,l,j,i),l=1,3),j=1,nlobi)
+ enddo
+ endif
+ enddo
+ endif
+#else
+C
+C Read scrot parameters for potentials determined from all-atom AM1 calculations
+C added by Urszula Kozlowska 07/11/2007
+C
+ do i=1,ntyp
+ read (irotam,*,end=112,err=112)
+ if (i.eq.10) then
+ read (irotam,*,end=112,err=112)
+ else
+ do j=1,65
+ read(irotam,*,end=112,err=112) sc_parmin(j,i)
+ enddo
+ endif
+ enddo
+#endif
+ close(irotam)
+#ifdef CRYST_TOR
+C
+C Read torsional parameters in old format
+C
+ read (itorp,*,end=113,err=113) ntortyp,nterm_old
+ write (iout,*) 'ntortyp,nterm',ntortyp,nterm_old
+ read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
+ do i=1,ntortyp
+ do j=1,ntortyp
+ read (itorp,'(a)',end=113,err=113)
+ do k=1,nterm_old
+ read (itorp,*,end=113,err=113) kk,v1(k,j,i),v2(k,j,i)
+ enddo
+ enddo
+ enddo
+ close (itorp)
+ if (lprint) then
+ write (iout,'(/a/)') 'Torsional constants:'
+ do i=1,ntortyp
+ do j=1,ntortyp
+ write (iout,'(2i3,6f10.5)') i,j,(v1(k,i,j),k=1,nterm_old)
+ write (iout,'(6x,6f10.5)') (v2(k,i,j),k=1,nterm_old)
+ enddo
+ enddo
+ endif
+
+
+#else
+C
+C Read torsional parameters
+C
+ read (itorp,*,end=113,err=113) ntortyp
+ read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
+ write (iout,*) 'ntortyp',ntortyp
+ do i=1,ntortyp
+ do j=1,ntortyp
+ read (itorp,*,end=113,err=113) nterm(i,j),nlor(i,j)
+ v0ij=0.0d0
+ si=-1.0d0
+ do k=1,nterm(i,j)
+ read (itorp,*,end=113,err=113) kk,v1(k,i,j),v2(k,i,j)
+ v0ij=v0ij+si*v1(k,i,j)
+ si=-si
+ enddo
+ do k=1,nlor(i,j)
+ read (itorp,*,end=113,err=113) kk,vlor1(k,i,j),vlor2(k,i,j),
+ & vlor3(k,i,j)
+ v0ij=v0ij+vlor1(k,i,j)/(1+vlor3(k,i,j)**2)
+ enddo
+ v0(i,j)=v0ij
+ enddo
+ enddo
+ close (itorp)
+ if (lprint) then
+ write (iout,'(/a/)') 'Torsional constants:'
+ do i=1,ntortyp
+ do j=1,ntortyp
+ write (iout,*) 'ityp',i,' jtyp',j
+ write (iout,*) 'Fourier constants'
+ do k=1,nterm(i,j)
+ write (iout,'(2(1pe15.5))') v1(k,i,j),v2(k,i,j)
+ enddo
+ write (iout,*) 'Lorenz constants'
+ do k=1,nlor(i,j)
+ write (iout,'(3(1pe15.5))')
+ & vlor1(k,i,j),vlor2(k,i,j),vlor3(k,i,j)
+ enddo
+ enddo
+ enddo
+ endif
+C
+C 6/23/01 Read parameters for double torsionals
+C
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
+ read (itordp,'(3a1)',end=112,err=112) t1,t2,t3
+ if (t1.ne.onelett(i) .or. t2.ne.onelett(j)
+ & .or. t3.ne.onelett(k)) then
+ write (iout,*) "Error in double torsional parameter file",
+ & i,j,k,t1,t2,t3
+ stop "Error in double torsional parameter file"
+ endif
+ read (itordp,*,end=114,err=114) ntermd_1(i,j,k),
+ & ntermd_2(i,j,k)
+ read (itordp,*,end=114,err=114) (v1c(1,l,i,j,k),
+ & l=1,ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1s(1,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1c(2,l,i,j,k),
+ & l=1,ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) (v1s(2,l,i,j,k),l=1,
+ & ntermd_1(i,j,k))
+ read (itordp,*,end=114,err=114) ((v2c(l,m,i,j,k),
+ & v2c(m,l,i,j,k),
+ & v2s(l,m,i,j,k),v2s(m,l,i,j,k),m=1,l-1),l=1,ntermd_2(i,j,k))
+ enddo
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) 'Constants for double torsionals'
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
+ write (iout,*) 'ityp',i,' jtyp',j,' ktyp',k,
+ & ' nsingle',ntermd_1(i,j,k),' ndouble',ntermd_2(i,j,k)
+ write (iout,*)
+ write (iout,*) 'Single angles:'
+ do l=1,ntermd_1(i,j,k)
+ write (iout,'(i5,2f10.5,5x,2f10.5)') l,
+ & v1c(1,l,i,j,k),v1s(1,l,i,j,k),
+ & v1c(2,l,i,j,k),v1s(2,l,i,j,k)
+ enddo
+ write (iout,*)
+ write (iout,*) 'Pairs of angles:'
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
+ do l=1,ntermd_2(i,j,k)
+ write (iout,'(i5,20f10.5)')
+ & l,(v2c(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ enddo
+ write (iout,*)
+ write (iout,'(3x,20i10)') (l,l=1,ntermd_2(i,j,k))
+ do l=1,ntermd_2(i,j,k)
+ write (iout,'(i5,20f10.5)')
+ & l,(v2s(l,m,i,j,k),m=1,ntermd_2(i,j,k))
+ enddo
+ write (iout,*)
+ enddo
+ enddo
+ enddo
+ endif
+#endif
+C Read of Side-chain backbone correlation parameters
+C Modified 11 May 2012 by Adasko
+CCC
+C
+ read (isccor,*,end=119,err=119) nsccortyp
+ read (isccor,*,end=119,err=119) (isccortyp(i),i=1,ntyp)
+c write (iout,*) 'ntortyp',ntortyp
+ maxinter=3
+cc maxinter is maximum interaction sites
+ do l=1,maxinter
+ do i=1,nsccortyp
+ do j=1,nsccortyp
+ read (isccor,*,end=119,err=119) nterm_sccor(i,j),
+ & nlor_sccor(i,j)
+ v0ijsccor=0.0d0
+ si=-1.0d0
+ do k=1,nterm_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,v1sccor(k,l,i,j)
+ & ,v2sccor(k,l,i,j)
+ v0ijsccor=v0ijsccor+si*v1sccor(k,l,i,j)
+ si=-si
+ enddo
+ do k=1,nlor_sccor(i,j)
+ read (isccor,*,end=119,err=119) kk,vlor1sccor(k,i,j),
+ & vlor2sccor(k,i,j),vlor3sccor(k,i,j)
+ v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/
+ &(1+vlor3sccor(k,i,j)**2)
+ enddo
+ v0sccor(i,j)=v0ijsccor
+ enddo
+ enddo
+ enddo
+ close (isccor)
+
+ if (lprint) then
+ write (iout,'(/a/)') 'Torsional constants:'
+ do i=1,nsccortyp
+ do j=1,nsccortyp
+ write (iout,*) 'ityp',i,' jtyp',j
+ write (iout,*) 'Fourier constants'
+ do k=1,nterm_sccor(i,j)
+ write(iout,'(2(1pe15.5))')(v1sccor(k,l,i,j),v2sccor(k,l,i,j),
+ & l=1,maxinter)
+ enddo
+ write (iout,*) 'Lorenz constants'
+ do k=1,nlor_sccor(i,j)
+ write (iout,'(3(1pe15.5))')
+ & vlor1sccor(k,i,j),vlor2sccor(k,i,j),vlor3sccor(k,i,j)
+ enddo
+ enddo
+ enddo
+ endif
+
+C
+C 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
+C interaction energy of the Gly, Ala, and Pro prototypes.
+C
+ read (ifourier,*,end=115,err=115) nloctyp
+ do i=1,nloctyp
+ read (ifourier,*,end=115,err=115)
+ read (ifourier,*,end=115,err=115) (b(ii,i),ii=1,13)
+#ifdef NEWCORR
+ read (ifourier,*,end=115,err=115) (bnew1(ii,1,i),ii=1,3)
+ read (ifourier,*,end=115,err=115) (bnew2(ii,1,i),ii=1,3)
+ read (ifourier,*,end=115,err=115) (bnew1(ii,2,i),ii=1,1)
+ read (ifourier,*,end=115,err=115) (bnew2(ii,2,i),ii=1,1)
+ read (ifourier,*,end=115,err=115) (eenew(ii,i),ii=1,1)
+#endif
+ if (lprint) then
+ write (iout,*) 'Type',i
+ write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
+ endif
+#ifdef NEWCORR
+ B1(1,i) = b(3,i)
+ B1(2,i) = b(5,i)
+ B1tilde(1,i) = b(3,i)
+ B1tilde(2,i) =-b(5,i)
+ B2(1,i) = b(2,i)
+ B2(2,i) = b(4,i)
+#endif
+ CC(1,1,i)= b(7,i)
+ CC(2,2,i)=-b(7,i)
+ CC(2,1,i)= b(9,i)
+ CC(1,2,i)= b(9,i)
+ Ctilde(1,1,i)=b(7,i)
+ Ctilde(1,2,i)=b(9,i)
+ Ctilde(2,1,i)=-b(9,i)
+ Ctilde(2,2,i)=b(7,i)
+ DD(1,1,i)= b(6,i)
+ DD(2,2,i)=-b(6,i)
+ DD(2,1,i)= b(8,i)
+ DD(1,2,i)= b(8,i)
+ Dtilde(1,1,i)=b(6,i)
+ Dtilde(1,2,i)=b(8,i)
+ Dtilde(2,1,i)=-b(8,i)
+ Dtilde(2,2,i)=b(6,i)
+#ifdef NEWCORR
+ EEold(1,1,i)= b(10,i)+b(11,i)
+ EEold(2,2,i)=-b(10,i)+b(11,i)
+ EEold(2,1,i)= b(12,i)-b(13,i)
+ EEold(1,2,i)= b(12,i)+b(13,i)
+ EEold(1,1,-i)= b(10,i)+b(11,i)
+ EEold(2,2,-i)=-b(10,i)+b(11,i)
+ EEold(2,1,-i)=-b(12,i)+b(13,i)
+ EEold(1,2,-i)=-b(12,i)-b(13,i)
+#else
+ EE(1,1,i)= b(10,i)+b(11,i)
+ EE(2,2,i)=-b(10,i)+b(11,i)
+ EE(2,1,i)= b(12,i)-b(13,i)
+ EE(1,2,i)= b(12,i)+b(13,i)
+#endif
+ enddo
+ if (lprint) then
+ do i=1,nloctyp
+ write (iout,*) 'Type',i
+ write (iout,*) 'B1'
+c write (iout,'(f10.5)') B1(:,i)
+ write(iout,*) B1(1,i),B1(2,i)
+ write (iout,*) 'B2'
+c write (iout,'(f10.5)') B2(:,i)
+ write(iout,*) B2(1,i),B2(2,i)
+ write (iout,*) 'CC'
+ do j=1,2
+ write (iout,'(2f10.5)') CC(j,1,i),CC(j,2,i)
+ enddo
+ write(iout,*) 'DD'
+ do j=1,2
+ write (iout,'(2f10.5)') DD(j,1,i),DD(j,2,i)
+ enddo
+ write(iout,*) 'EE'
+ do j=1,2
+ write (iout,'(2f10.5)') EE(j,1,i),EE(j,2,i)
+ enddo
+ enddo
+ endif
+C
+C Read electrostatic-interaction parameters
+C
+ if (lprint) then
+ write (iout,'(/a)') 'Electrostatic interaction constants:'
+ write (iout,'(1x,a,1x,a,10x,a,11x,a,11x,a,11x,a)')
+ & 'IT','JT','APP','BPP','AEL6','AEL3'
+ endif
+ read (ielep,*,end=116,err=116) ((epp(i,j),j=1,2),i=1,2)
+ read (ielep,*,end=116,err=116) ((rpp(i,j),j=1,2),i=1,2)
+ read (ielep,*,end=116,err=116) ((elpp6(i,j),j=1,2),i=1,2)
+ read (ielep,*,end=116,err=116) ((elpp3(i,j),j=1,2),i=1,2)
+ close (ielep)
+ do i=1,2
+ do j=1,2
+ rri=rpp(i,j)**6
+ app (i,j)=epp(i,j)*rri*rri
+ bpp (i,j)=-2.0D0*epp(i,j)*rri
+ ael6(i,j)=elpp6(i,j)*4.2D0**6
+ ael3(i,j)=elpp3(i,j)*4.2D0**3
+ if (lprint) write(iout,'(2i3,4(1pe15.4))')i,j,app(i,j),bpp(i,j),
+ & ael6(i,j),ael3(i,j)
+ enddo
+ enddo
+C
+C Read side-chain interaction parameters.
+C
+ read (isidep,*,end=117,err=117) ipot,expon
+ if (ipot.lt.1 .or. ipot.gt.6) then
+ write (iout,'(2a)') 'Error while reading SC interaction',
+ & 'potential file - unknown potential type.'
+ stop
+ endif
+ expon2=expon/2
+ write(iout,'(/3a,2i3)') 'Potential is ',potname(ipot),
+ & ', exponents are ',expon,2*expon
+ goto (10,20,30,30,40,50) ipot
+C----------------------- LJ potential ---------------------------------
+ 10 read (isidep,*,end=117,err=117)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ & (sigma0(i),i=1,ntyp)
+ if (lprint) then
+ write (iout,'(/a/)') 'Parameters of the LJ potential:'
+ write (iout,'(a/)') 'The epsilon array:'
+ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
+ write (iout,'(/a)') 'One-body parameters:'
+ write (iout,'(a,4x,a)') 'residue','sigma'
+ write (iout,'(a3,6x,f10.5)') (restyp(i),sigma0(i),i=1,ntyp)
+ endif
+ goto 60
+C----------------------- LJK potential --------------------------------
+ 20 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ & (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp)
+ if (lprint) then
+ write (iout,'(/a/)') 'Parameters of the LJK potential:'
+ write (iout,'(a/)') 'The epsilon array:'
+ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
+ write (iout,'(/a)') 'One-body parameters:'
+ write (iout,'(a,4x,2a)') 'residue',' sigma ',' r0 '
+ write (iout,'(a3,6x,2f10.5)') (restyp(i),sigma0(i),rr0(i),
+ & i=1,ntyp)
+ endif
+ goto 60
+C---------------------- GB or BP potential -----------------------------
+ 30 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ & (sigma0(i),i=1,ntyp),(sigii(i),i=1,ntyp),(chip0(i),i=1,ntyp),
+ & (alp(i),i=1,ntyp)
+C For the GB potential convert sigma'**2 into chi'
+ if (ipot.eq.4) then
+ do i=1,ntyp
+ chip(i)=(chip0(i)-1.0D0)/(chip0(i)+1.0D0)
+ enddo
+ endif
+ if (lprint) then
+ write (iout,'(/a/)') 'Parameters of the BP potential:'
+ write (iout,'(a/)') 'The epsilon array:'
+ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
+ write (iout,'(/a)') 'One-body parameters:'
+ write (iout,'(a,4x,4a)') 'residue',' sigma ','s||/s_|_^2',
+ & ' chip ',' alph '
+ write (iout,'(a3,6x,4f10.5)') (restyp(i),sigma0(i),sigii(i),
+ & chip(i),alp(i),i=1,ntyp)
+ endif
+ goto 60
+C--------------------- GBV potential -----------------------------------
+ 40 read (isidep,*,end=116,err=116)((eps(i,j),j=i,ntyp),i=1,ntyp),
+ & (sigma0(i),i=1,ntyp),(rr0(i),i=1,ntyp),(sigii(i),i=1,ntyp),
+ & (chip(i),i=1,ntyp),(alp(i),i=1,ntyp)
+ if (lprint) then
+ write (iout,'(/a/)') 'Parameters of the GBV potential:'
+ write (iout,'(a/)') 'The epsilon array:'
+ call printmat(ntyp,ntyp,ntyp,iout,restyp,eps)
+ write (iout,'(/a)') 'One-body parameters:'
+ write (iout,'(a,4x,5a)') 'residue',' sigma ',' r0 ',
+ & 's||/s_|_^2',' chip ',' alph '
+ write (iout,'(a3,6x,5f10.5)') (restyp(i),sigma0(i),rr0(i),
+ & sigii(i),chip(i),alp(i),i=1,ntyp)
+ endif
+ goto 60
+C--------------------- Momo potential -----------------------------------
+
+ 50 continue
+
+ read (isidep,*,end=116,err=116) (icharge(i),i=1,ntyp)
+c write (2,*) "icharge",(icharge(i),i=1,ntyp)
+ do i=1,ntyp
+ do j=1,i
+c! write (*,*) "Im in ", i, " ", j
+ read(isidep,*,end=116,err=116)
+ & eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i),
+ & (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j),
+ & chis(i,j),chis(j,i),
+ & nstate(i,j),(wstate(k,i,j),k=1,4),
+ & dhead(1,1,i,j),
+ & dhead(1,2,i,j),
+ & dhead(2,1,i,j),
+ & dhead(2,2,i,j),
+ & dtail(1,i,j),dtail(2,i,j),
+ & epshead(i,j),sig0head(i,j),
+ & rborn(i,j),rborn(j,i),
+ & (wqdip(k,i,j),k=1,2),wquad(i,j),
+ & alphapol(i,j),alphapol(j,i),
+ & (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j)
+ END DO
+ END DO
+c! write (*,*) "nstate gly-gly", nstate(10,10)
+c! THIS LOOP FILLS PARAMETERS FOR PAIRS OF AA's NOT EXPLICITLY
+c! DEFINED IN SCPARM.MOMO. IT DOES SO BY TAKING THEM FROM SYMMETRIC
+c! PAIR, FOR EG. IF ARG-HIS IS BLANK, IT WILL TAKE PARAMETERS
+c! FROM HIS-ARG.
+c!
+c! DISABLE IT AT >>YOUR OWN PERIL<<
+c!
+ DO i = 1, ntyp
+ DO j = i+1, ntyp
+ eps(i,j) = eps(j,i)
+ sigma(i,j) = sigma(j,i)
+ nstate(i,j) = nstate(j,i)
+ sigmap1(i,j) = sigmap1(j,i)
+ sigmap2(i,j) = sigmap2(j,i)
+ sigiso1(i,j) = sigiso1(j,i)
+ sigiso2(i,j) = sigiso2(j,i)
+
+ DO k = 1, 4
+ alphasur(k,i,j) = alphasur(k,j,i)
+ wstate(k,i,j) = wstate(k,j,i)
+ alphiso(k,i,j) = alphiso(k,j,i)
+ END DO
+
+ dhead(2,1,i,j) = dhead(1,1,j,i)
+ dhead(2,2,i,j) = dhead(1,2,j,i)
+ dhead(1,1,i,j) = dhead(2,1,j,i)
+ dhead(1,2,i,j) = dhead(2,2,j,i)
+ dtail(1,i,j) = dtail(1,j,i)
+ dtail(2,i,j) = dtail(2,j,i)
+c! DO k = 1, 2
+c! DO l = 1, 2
+c! write (*,*) "dhead(k,l,j,i) = ", dhead(k,l,j,i)
+c! write (*,*) "dhead(k,l,i,j) = ", dhead(k,l,i,j)
+c! dhead(l,k,i,j) = dhead(k,l,j,i)
+c! END DO
+c! END DO
+
+ epshead(i,j) = epshead(j,i)
+ sig0head(i,j) = sig0head(j,i)
+
+ DO k = 1, 2
+ wqdip(k,i,j) = wqdip(k,j,i)
+ END DO
+
+ wquad(i,j) = wquad(j,i)
+ epsintab(i,j) = epsintab(j,i)
+
+ END DO
+ END DO
+
+ if (.not.lprint) goto 70
+ write (iout,'(a)')
+ & "Parameters of the new physics-based SC-SC interaction potential"
+ write (iout,'(/7a)') 'Residues',' epsGB',' rGB',
+ & ' chi1GB',' chi2GB',' chip1GB',' chip2GB'
+ do i=1,ntyp
+ do j=1,i
+ write (iout,'(2(a3,1x),1pe10.3,5(0pf10.3))')
+ & restyp(i),restyp(j),eps(i,j),sigma(i,j),chi(i,j),chi(j,i),
+ & chipp(i,j),chipp(j,i)
+ enddo
+ enddo
+ write (iout,'(/9a)') 'Residues',' alphasur1',' alphasur2',
+ & ' alphasur3',' alphasur4',' sigmap1',' sigmap2',
+ & ' chis1',' chis2'
+ do i=1,ntyp
+ do j=1,i
+ write (iout,'(2(a3,1x),8(0pf10.3))')
+ & restyp(i),restyp(j),(alphasur(k,i,j),k=1,4),
+ & sigmap1(i,j),sigmap2(j,i),chis(i,j),chis(j,i)
+ enddo
+ enddo
+ write (iout,'(/14a)') 'Residues',' nst ',' wst1',
+ & ' wst2',' wst3',' wst4',' dh11',' dh21',
+ & ' dh12',' dh22',' dt1',' dt2',' epsh1',
+ & ' sigh'
+ do i=1,ntyp
+ do j=1,i
+ write (iout,'(2(a3,1x),i3,4f8.3,6f7.2,f9.5,f7.2)')
+ & restyp(i),restyp(j),nstate(i,j),(wstate(k,i,j),k=1,4),
+ & ((dhead(l,k,i,j),l=1,2),k=1,2),dtail(1,i,j),dtail(2,i,j),
+ & epshead(i,j),sig0head(i,j)
+ enddo
+ enddo
+ write (iout,'(/12a)') 'Residues',' ch1',' ch2',
+ & ' rborn1',' rborn2',' wqdip1',' wqdip2',
+ & ' wquad'
+ do i=1,ntyp
+ do j=1,i
+ write (iout,'(2(a3,1x),2i4,5f10.3)')
+ & restyp(i),restyp(j),icharge(i),icharge(j),
+ & rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j)
+ enddo
+ enddo
+ write (iout,'(/12a)') 'Residues',
+ & ' alphpol1',
+ & ' alphpol2',' alphiso1',' alpiso2',
+ & ' alpiso3',' alpiso4',' sigiso1',' sigiso2',
+ & ' epsin'
+ do i=1,ntyp
+ do j=1,i
+ write (iout,'(2(a3,1x),11f10.3)')
+ & restyp(i),restyp(j),alphapol(i,j),alphapol(j,i),
+ & (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(j,i),
+ & epsintab(i,j)
+ enddo
+ enddo
+ goto 70
+
+ 60 continue
+ close (isidep)
+C-----------------------------------------------------------------------
+C Calculate the "working" parameters of SC interactions.
+
+ IF (ipot.LT.6) THEN
+ do i=1,ntyp
+ do j=i,ntyp
+ sigma(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)
+ sigma(j,i)=sigma(i,j)
+ rs0(i,j)=dwa16*sigma(i,j)
+ rs0(j,i)=rs0(i,j)
+ enddo
+ enddo
+ END IF
+
+ 70 continue
+ write (iout,*) "IPOT=",ipot
+ if (lprint) write (iout,'(/a/10x,7a/72(1h-))')
+ & 'Working parameters of the SC interactions:',
+ & ' a ',' b ',' augm ',' sigma ',' r0 ',
+ & ' chi1 ',' chi2 '
+ do i=1,ntyp
+ do j=i,ntyp
+ epsij=eps(i,j)
+ if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4 .or. ipot.eq.6 ) THEN
+ rrij=sigma(i,j)
+ else
+ rrij=rr0(i)+rr0(j)
+ endif
+ r0(i,j)=rrij
+ r0(j,i)=rrij
+ rrij=rrij**expon
+ epsij=eps(i,j)
+ sigeps=dsign(1.0D0,epsij)
+ epsij=dabs(epsij)
+ aa(i,j)=epsij*rrij*rrij
+ bb(i,j)=-sigeps*epsij*rrij
+ aa(j,i)=aa(i,j)
+ bb(j,i)=bb(i,j)
+ IF ((ipot.gt.2).AND.(ipot.LT.6)) THEN
+ sigt1sq=sigma0(i)**2
+ sigt2sq=sigma0(j)**2
+ sigii1=sigii(i)
+ sigii2=sigii(j)
+ ratsig1=sigt2sq/sigt1sq
+ ratsig2=1.0D0/ratsig1
+ chi(i,j)=(sigii1-1.0D0)/(sigii1+ratsig1)
+ if (j.gt.i) chi(j,i)=(sigii2-1.0D0)/(sigii2+ratsig2)
+ rsum_max=dsqrt(sigii1*sigt1sq+sigii2*sigt2sq)
+ else
+ rsum_max=sigma(i,j)
+ endif
+c if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
+ sigmaii(i,j)=rsum_max
+ sigmaii(j,i)=rsum_max
+c else
+c sigmaii(i,j)=r0(i,j)
+c sigmaii(j,i)=r0(i,j)
+c endif
+cd write (iout,*) i,j,r0(i,j),sigma(i,j),rsum_max
+ if ((ipot.eq.2 .or. ipot.eq.5) .and. r0(i,j).gt.rsum_max) then
+ r_augm=sigma(i,j)*(rrij-sigma(i,j))/rrij
+ augm(i,j)=epsij*r_augm**(2*expon)
+c augm(i,j)=0.5D0**(2*expon)*aa(i,j)
+ augm(j,i)=augm(i,j)
+ else
+ augm(i,j)=0.0D0
+ augm(j,i)=0.0D0
+ endif
+ if (lprint) then
+ if (ipot.lt.6) then
+ write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))')
+ & restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),
+ & sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
+ else
+ write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3),2i3,10f8.4,
+ & i3,40f10.4)')
+ & restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),
+ & sigma(i,j),r0(i,j),chi(i,j),chi(j,i),
+ & icharge(i),icharge(j),chipp(i,j),chipp(j,i),
+ & (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(j,i),
+ & chis(i,j),chis(j,i),
+ & nstate(i,j),(wstate(k,i,j),k=1,4),
+ & ((dhead(l,k,i,j),l=1,2),k=1,2),dtail(1,i,j),dtail(2,i,j),
+ & epshead(i,j),sig0head(i,j),
+ & rborn(i,j),(wqdip(k,i,j),k=1,2),wquad(i,j),
+ & alphapol(i,j),alphapol(j,i),
+ & (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j)
+
+ endif
+ endif
+ enddo
+ enddo
+
+C
+C Define the SC-p interaction constants
+C
+#ifdef OLDSCP
+ do i=1,20
+C "Soft" SC-p repulsion (causes helices to be too flat, but facilitates
+C helix formation)
+c aad(i,1)=0.3D0*4.0D0**12
+C Following line for constants currently implemented
+C "Hard" SC-p repulsion (gives correct turn spacing in helices)
+ aad(i,1)=1.5D0*4.0D0**12
+c aad(i,1)=0.17D0*5.6D0**12
+ aad(i,2)=aad(i,1)
+C "Soft" SC-p repulsion
+ bad(i,1)=0.0D0
+C Following line for constants currently implemented
+c aad(i,1)=0.3D0*4.0D0**6
+C "Hard" SC-p repulsion
+ bad(i,1)=3.0D0*4.0D0**6
+c bad(i,1)=-2.0D0*0.17D0*5.6D0**6
+ bad(i,2)=bad(i,1)
+c aad(i,1)=0.0D0
+c aad(i,2)=0.0D0
+c bad(i,1)=1228.8D0
+c bad(i,2)=1228.8D0
+ enddo
+#else
+C
+C 8/9/01 Read the SC-p interaction constants from file
+C
+ do i=1,ntyp
+ read (iscpp,*,end=118,err=118) (eps_scp(i,j),rscp(i,j),j=1,2)
+ enddo
+ do i=1,ntyp
+ aad(i,1)=dabs(eps_scp(i,1))*rscp(i,1)**12
+ aad(i,2)=dabs(eps_scp(i,2))*rscp(i,2)**12
+ bad(i,1)=-2*eps_scp(i,1)*rscp(i,1)**6
+ bad(i,2)=-2*eps_scp(i,2)*rscp(i,2)**6
+ enddo
+
+ if (lprint) then
+ write (iout,*) "Parameters of SC-p interactions:"
+ do i=1,20
+ write (iout,'(4f8.3,4e12.4)') eps_scp(i,1),rscp(i,1),
+ & eps_scp(i,2),rscp(i,2),aad(i,1),bad(i,1),aad(i,2),bad(i,2)
+ enddo
+ endif
+#endif
+C
+C Define the constants of the disulfide bridge
+C
+ ebr=-5.50D0
+c
+c Old arbitrary potential - commented out.
+c
+c dbr= 4.20D0
+c fbr= 3.30D0
+c
+c Constants of the disulfide-bond potential determined based on the RHF/6-31G**
+c energy surface of diethyl disulfide.
+c A. Liwo and U. Kozlowska, 11/24/03
+c
+ D0CM = 3.78d0
+ AKCM = 15.1d0
+ AKTH = 11.0d0
+ AKCT = 12.0d0
+ V1SS =-1.08d0
+ V2SS = 7.61d0
+ V3SS = 13.7d0
+
+ if (lprint) then
+ write (iout,'(/a)') "Disulfide bridge parameters:"
+ write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
+ write (iout,'(2(a,f10.2))') 'd0cm:',d0cm,' akcm:',akcm
+ write (iout,'(2(a,f10.2))') 'akth:',akth,' akct:',akct
+ write (iout,'(3(a,f10.2))') 'v1ss:',v1ss,' v2ss:',v2ss,
+ & ' v3ss:',v3ss
+ endif
+ return
+ 110 write (iout,*) "Error reading bond energy parameters."
+ goto 999
+ 111 write (iout,*) "Error reading bending energy parameters."
+ goto 999
+ 112 write (iout,*) "Error reading rotamer energy parameters."
+ goto 999
+ 113 write (iout,*) "Error reading torsional energy parameters."
+ goto 999
+ 114 write (iout,*) "Error reading double torsional energy parameters."
+ goto 999
+ 115 write (iout,*)
+ & "Error reading cumulant (multibody energy) parameters."
+ goto 999
+ 116 write (iout,*) "Error reading electrostatic energy parameters."
+ goto 999
+ 117 write (iout,*) "Error reading side chain interaction parameters."
+ goto 999
+ 118 write (iout,*) "Error reading SCp interaction parameters."
+ goto 999
+ 119 write (iout,*) "Error reading SCCOR parameters"
+ 999 continue
+#ifdef MPI
+ call MPI_Finalize(Ierror)
+#endif
+ stop
+ end
--- /dev/null
+ double precision function pinorm(x)
+ implicit real*8 (a-h,o-z)
+c
+c this function takes an angle (in radians) and puts it in the range of
+c -pi to +pi.
+c
+ integer n
+ include 'COMMON.GEO'
+ n = x / dwapi
+ pinorm = x - n * dwapi
+ if ( pinorm .gt. pi ) then
+ pinorm = pinorm - dwapi
+ else if ( pinorm .lt. - pi ) then
+ pinorm = pinorm + dwapi
+ end if
+ return
+ end
--- /dev/null
+ subroutine printmat(ldim,m,n,iout,key,a)
+ character*3 key(n)
+ double precision a(ldim,n)
+ do 1 i=1,n,8
+ nlim=min0(i+7,n)
+ write (iout,1000) (key(k),k=i,nlim)
+ write (iout,1020)
+ 1000 format (/5x,8(6x,a3))
+ 1020 format (/80(1h-)/)
+ do 2 j=1,n
+ write (iout,1010) key(j),(a(j,k),k=i,nlim)
+ 2 continue
+ 1 continue
+ 1010 format (a3,2x,8(f9.4))
+ return
+ end
--- /dev/null
+ subroutine proc_cont
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.CONTACTS1'
+ include 'COMMON.PEPTCONT'
+ include 'COMMON.GEO'
+ write (iout,*) "proc_cont: nlevel",nlevel
+ if (nlevel.lt.0) then
+ write (iout,*) "call define_fragments"
+ call define_fragments
+ else
+ write (iout,*) "call secondary2"
+ call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,
+ & isec_ref)
+ endif
+ write (iout,'(80(1h=))')
+ write (iout,*) "Electrostatic contacts"
+ call contacts_between_fragments(.true.,0,ncont_pept_ref,
+ & icont_pept_ref,ncont_frag_ref(1),icont_frag_ref(1,1,1))
+ write (iout,'(80(1h=))')
+ write (iout,*) "Side chain contacts"
+ call contacts_between_fragments(.true.,0,ncont_ref,
+ & icont_ref,nsccont_frag_ref(1),isccont_frag_ref(1,1,1))
+ if (nlevel.lt.0) then
+ do i=1,nfrag(1)
+ ind=icant(i,i)
+ len_cut=1000
+ if (istruct(i).le.1) then
+ len_cut=max0(len_frag(i,1)*4/5,3)
+ else if (istruct(i).eq.2 .or. istruct(i).eq.4) then
+ len_cut=max0(len_frag(i,1)*2/5,3)
+ endif
+ write (iout,*) "i",i," istruct",istruct(i)," ncont_frag",
+ & ncont_frag_ref(ind)," len_cut",len_cut,
+ & " icont_single",icont_single," iloc_single",iloc_single
+ iloc(i)=iloc_single
+ if (iloc(i).gt.0) write (iout,*)
+ & "Local structure used to compare structure of fragment",i,
+ & " to native."
+ if (istruct(i).ne.3 .and. istruct(i).ne.0
+ & .and. icont_single.gt.0 .and.
+ & ncont_frag_ref(ind).ge.len_cut) then
+ write (iout,*) "Electrostatic contacts used to compare",
+ & " structure of fragment",i," to native."
+ ielecont(i,1)=1
+ isccont(i,1)=0
+ else if (icont_single.gt.0 .and. nsccont_frag_ref(ind)
+ & .ge.len_cut) then
+ write (iout,*) "Side chain contacts used to compare",
+ & " structure of fragment",i," to native."
+ isccont(i,1)=1
+ ielecont(i,1)=0
+ else
+ write (iout,*) "Contacts not used to compare",
+ & " structure of fragment",i," to native."
+ ielecont(i,1)=0
+ isccont(i,1)=0
+ nc_req_setf(i,1)=0
+ endif
+ if (irms_single.gt.0 .or. isccont(i,1).eq.0
+ & .and. ielecont(i,1).eq.0) then
+ write (iout,*) "RMSD used to compare",
+ & " structure of fragment",i," to native."
+ irms(i,1)=1
+ else
+ write (iout,*) "RMSD not used to compare",
+ & " structure of fragment",i," to native."
+ irms(i,1)=0
+ endif
+ enddo
+ endif
+ if (nlevel.lt.-1) then
+ call define_pairs
+ nlevel = -nlevel
+ if (nlevel.gt.3) nlevel=3
+ if (nlevel.eq.3) then
+ nfrag(3)=1
+ npiece(1,3)=nfrag(1)
+ do i=1,nfrag(1)
+ ipiece(i,1,3)=i
+ enddo
+ ielecont(1,3)=0
+ isccont(1,3)=0
+ irms(1,3)=1
+ n_shift(1,1,3)=0
+ n_shift(2,1,3)=0
+ endif
+ else if (nlevel.eq.-1) then
+ nlevel=1
+ endif
+ isnfrag(1)=0
+ do i=1,nlevel
+ isnfrag(i+1)=isnfrag(i)+nfrag(i)
+ enddo
+ ndigit=3*nfrag(1)
+ do i=2,nlevel
+ ndigit=ndigit+2*nfrag(i)
+ enddo
+ write (iout,*) "ndigit",ndigit
+ if (.not.binary .and. ndigit.gt.30) then
+ write (iout,*) "Highest class too large; switching to",
+ & " binary representation."
+ binary=.true.
+ endif
+ write (iout,*) "isnfrag",(isnfrag(i),i=1,nlevel+1)
+ write(iout,*) "rmscut_base_up",rmscut_base_up,
+ & " rmscut_base_low",rmscut_base_low," rmsup_lim",rmsup_lim
+ do i=1,nlevel
+ do j=1,nfrag(i)
+ length_frag = 0
+ if (i.eq.1) then
+ do k=1,npiece(j,i)
+ length_frag=length_frag+ifrag(2,k,j)-ifrag(1,k,j)+1
+ enddo
+ else
+ do k=1,npiece(j,i)
+ length_frag=length_frag+len_frag(ipiece(k,j,i),1)
+ enddo
+ endif
+ len_frag(j,i)=length_frag
+ rmscutfrag(1,j,i)=rmscut_base_up*length_frag
+ rmscutfrag(2,j,i)=rmscut_base_low*length_frag
+ if (rmscutfrag(1,j,i).lt.rmsup_lim)
+ & rmscutfrag(1,j,i)=rmsup_lim
+ if (rmscutfrag(1,j,i).gt.rmsupup_lim)
+ & rmscutfrag(1,j,i)=rmsupup_lim
+ enddo
+ enddo
+ write (iout,*) "Level",1," number of fragments:",nfrag(1)
+ do j=1,nfrag(1)
+ write (iout,*) npiece(j,1),(ifrag(1,k,j),ifrag(2,k,j),
+ & k=1,npiece(j,1)),len_frag(j,1),rmscutfrag(1,j,1),
+ & rmscutfrag(2,j,1),n_shift(1,j,1),n_shift(2,j,1),
+ & ang_cut(j)*rad2deg,ang_cut1(j)*rad2deg,frac_min(j),
+ & nc_fragm(j,1),nc_req_setf(j,1),istruct(j)
+ enddo
+ do i=2,nlevel
+ write (iout,*) "Level",i," number of fragments:",nfrag(i)
+ do j=1,nfrag(i)
+ write (iout,*) npiece(j,i),(ipiece(k,j,i),
+ & k=1,npiece(j,i)),len_frag(j,i),rmscutfrag(1,j,i),
+ & rmscutfrag(2,j,i),n_shift(1,j,i),n_shift(2,j,i),
+ & nc_fragm(j,i),nc_req_setf(j,i)
+ enddo
+ enddo
+ return
+ end
--- /dev/null
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+
+#ifdef LINUX
+#ifdef PGI
+void proc_proc_(long int *f, int *i)
+#else
+void proc_proc__(long int *f, int *i)
+#endif
+#endif
+#ifdef SGI
+void proc_proc_(long int *f, int *i)
+#endif
+#ifdef WIN
+void _stdcall PROC_PROC(long int *f, int *i)
+#endif
+#if defined(AIX) || defined(WINPGI)
+void proc_proc(long int *f, int *i)
+#endif
+
+{
+static long int NaNQ;
+static long int NaNQm;
+
+if(*i==-1)
+ {
+ NaNQ=*f;
+ NaNQm=0xffffffff;
+ return;
+ }
+*i=0;
+if(*f==NaNQ)
+ *i=1;
+if(*f==NaNQm)
+ *i=1;
+}
+
+
+#ifdef LINUX
+void proc_conv__(char *buf, int *i, int n)
+#endif
+#ifdef SGI
+void proc_conv_(char *buf, int *i, int n)
+#endif
+#if defined(AIX) || defined(WINPGI)
+void proc_conv(char *buf, int *i, int n)
+#endif
+#ifdef WIN
+void _stdcall PROC_CONV(char *buf, int *i, int n)
+#endif
+{
+int j;
+
+sscanf(buf,"%d",&j);
+*i=j;
+return;
+}
+
+#ifdef LINUX
+void proc_conv_r__(char *buf, int *i, int n)
+#endif
+#ifdef SGI
+void proc_conv_r_(char *buf, int *i, int n)
+#endif
+#if defined(AIX) || defined(WINPGI)
+void proc_conv_r(char *buf, int *i, int n)
+#endif
+#ifdef WIN
+void _stdcall PROC_CONV_R(char *buf, int *i, int n)
+#endif
+
+{
+
+/* sprintf(buf,"%d",*i); */
+
+return;
+}
+
+#ifndef IMSL
+#ifdef LINUX
+void dsvrgp__(int *n, double *tab1, double *tab2, int *itab)
+#endif
+#ifdef SGI
+void dsvrgp_(int *n, double *tab1, double *tab2, int *itab)
+#endif
+#if defined(AIX) || defined(WINPGI)
+void dsvrgp(int *n, double *tab1, double *tab2, int *itab)
+#endif
+#ifdef WIN
+void _stdcall DSVRGP(int *n, double *tab1, double *tab2, int *itab)
+#endif
+{
+double t;
+int i,j,k;
+
+if(tab1 != tab2)
+ {
+ for(i=0; i<*n; i++)
+ tab2[i]=tab1[i];
+ }
+k=0;
+while(k<*n-1)
+ {
+ j=k;
+ t=tab2[k];
+ for(i=k+1; i<*n; i++)
+ if(t>tab2[i])
+ {
+ j=i;
+ t=tab2[i];
+ }
+ if(j!=k)
+ {
+ tab2[j]=tab2[k];
+ tab2[k]=t;
+ i=itab[j];
+ itab[j]=itab[k];
+ itab[k]=i;
+ }
+ k++;
+ }
+}
+#endif
--- /dev/null
+ subroutine promienie(*)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CONTPAR'
+ include 'COMMON.LOCAL'
+ integer i,j
+ real*8 facont /1.569D0/ ! facont = (2/(1-sqrt(1-1/4)))**(1/6)
+ character*8 contfunc
+ character*8 contfuncid(5)/'GB','DIST','CEN','ODC','SIG'/
+ character*8 ucase
+ call getenv("CONTFUNC",contfunc)
+ contfunc=ucase(contfunc)
+ do icomparfunc=1,5
+ if (contfunc.eq.contfuncid(icomparfunc)) goto 10
+ enddo
+ 10 continue
+ write (iout,*) "Sidechain contact function is ",contfunc,
+ & "icomparfunc",icomparfunc
+ do i=1,ntyp
+ do j=1,ntyp
+ if (icomparfunc.lt.3) then
+ read(isidep1,*) chi_comp(i,j),chip_comp(i,j),sig_comp(i,j),
+ & sc_cutoff(i,j)
+ else if (icomparfunc.lt.5) then
+ read(isidep1,*) sc_cutoff(i,j)
+ else if (icomparfunc.eq.5) then
+ sc_cutoff(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)*facont
+ else
+ write (iout,*) "Error - Unknown contact function"
+ return1
+ endif
+ enddo
+ enddo
+ close (isidep1)
+ do i=1,ntyp1
+ if (i.eq.10 .or. i.eq.21) then
+ dsc_inv(i)=0.0d0
+ else
+ dsc_inv(i)=1.0d0/dsc(i)
+ endif
+ enddo
+ return
+ end
--- /dev/null
+ double precision function qwolynes(ilevel,jfrag)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ integer ilevel,jfrag
+ integer i,j,jl,k,l,il,kl,nl,np,ip,kp
+ integer nsep /3/
+ double precision dist
+ double precision qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM
+ logical lprn /.false./
+ double precision sigm,x
+ sigm(x)=0.25d0*x
+c write (iout,*) "QWolyes: " jfrag",jfrag,
+c & " ilevel",ilevel
+ qq = 0.0d0
+ if (ilevel.eq.0) then
+ if (lprn) write (iout,*) "Q computed for whole molecule"
+ nl=0
+ do il=nnt+nsep,nct
+ do jl=nnt,il-nsep
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ nl=nl+1
+ d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+
+ & (cref(2,jl)-cref(2,il))**2+
+ & (cref(3,jl)-cref(3,il))**2)
+ dij=dist(il,jl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt(
+ & (cref(1,jl+nres)-cref(1,il+nres))**2+
+ & (cref(2,jl+nres)-cref(2,il+nres))**2+
+ & (cref(3,jl+nres)-cref(3,il+nres))**2)
+ dijCM=dist(il+nres,jl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "il",il," jl",jl,
+ & " itype",itype(il),itype(jl)
+ write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,
+ & " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ enddo
+ enddo
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else if (ilevel.eq.1) then
+ if (lprn) write (iout,*) "Level",ilevel," fragment",jfrag
+ nl=0
+c write (iout,*) "nlist_frag",nlist_frag(jfrag)
+ do i=2,nlist_frag(jfrag)
+ do j=1,i-1
+ il=list_frag(i,jfrag)
+ jl=list_frag(j,jfrag)
+ if (iabs(il-jl).gt.nsep) then
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ nl=nl+1
+ d0ij=dsqrt((cref(1,jl)-cref(1,il))**2+
+ & (cref(2,jl)-cref(2,il))**2+
+ & (cref(3,jl)-cref(3,il))**2)
+ dij=dist(il,jl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt(
+ & (cref(1,jl+nres)-cref(1,il+nres))**2+
+ & (cref(2,jl+nres)-cref(2,il+nres))**2+
+ & (cref(3,jl+nres)-cref(3,il+nres))**2)
+ dijCM=dist(il+nres,jl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/(sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "i",i," j",j," il",il," jl",jl,
+ & " itype",itype(il),itype(jl)
+ write (iout,*)"d0ij",d0ij," dij",dij," d0ijCM",d0ijCM,
+ & " dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ endif
+ enddo
+ enddo
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else if (ilevel.eq.2) then
+ np=npiece(jfrag,ilevel)
+ nl=0
+ do i=2,np
+ ip=ipiece(i,jfrag,ilevel)
+ do j=1,nlist_frag(ip)
+ il=list_frag(j,ip)
+ do k=1,i-1
+ kp=ipiece(k,jfrag,ilevel)
+ do l=1,nlist_frag(kp)
+ kl=list_frag(l,kp)
+ if (iabs(kl-il).gt.nsep) then
+ nl=nl+1
+ dij=0.0d0
+ dijCM=0.0d0
+ d0ij=0.0d0
+ d0ijCM=0.0d0
+ qqij=0.0d0
+ qqijCM=0.0d0
+ d0ij=dsqrt((cref(1,kl)-cref(1,il))**2+
+ & (cref(2,kl)-cref(2,il))**2+
+ & (cref(3,kl)-cref(3,il))**2)
+ dij=dist(il,kl)
+ qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
+ if (itype(il).ne.10 .or. itype(kl).ne.10) then
+ nl=nl+1
+ d0ijCM=dsqrt(
+ & (cref(1,kl+nres)-cref(1,il+nres))**2+
+ & (cref(2,kl+nres)-cref(2,il+nres))**2+
+ & (cref(3,kl+nres)-cref(3,il+nres))**2)
+ dijCM=dist(il+nres,kl+nres)
+ qqijCM = dexp(-0.5d0*((dijCM-d0ijCM)/
+ & (sigm(d0ijCM)))**2)
+ endif
+ qq = qq+qqij+qqijCM
+ if (lprn) then
+ write (iout,*) "i",i," j",j," k",k," l",l," il",il,
+ & " kl",kl," itype",itype(il),itype(kl)
+ write (iout,*) " d0ij",d0ij," dij",dij," d0ijCM",
+ & d0ijCM," dijCM",dijCM," qqij",qqij," qqijCM",qqijCM
+ endif
+ endif
+ enddo ! l
+ enddo ! k
+ enddo ! j
+ enddo ! i
+ qq = qq/nl
+ if (lprn) write (iout,*) "nl",nl," qq",qq
+ else
+ write (iout,*)"Error: Q can be computed only for level 1 and 2."
+ endif
+ qwolynes=1.0d0-qq
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine fragment_list
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ logical lprn /.true./
+ integer i,ilevel,j,k,jfrag
+ do jfrag=1,nfrag(1)
+ nlist_frag(jfrag)=0
+ do i=1,npiece(jfrag,1)
+ if (lprn) write (iout,*) "jfrag=",jfrag,
+ & "i=",i," fragment",ifrag(1,i,jfrag),
+ & ifrag(2,i,jfrag)
+ do j=ifrag(1,i,jfrag),ifrag(2,i,jfrag)
+ do k=1,nlist_frag(jfrag)
+ if (list_frag(k,jfrag).eq.j) goto 10
+ enddo
+ nlist_frag(jfrag)=nlist_frag(jfrag)+1
+ list_frag(nlist_frag(jfrag),jfrag)=j
+ enddo
+ 10 continue
+ enddo
+ enddo
+ write (iout,*) "Fragment list"
+ do j=1,nfrag(1)
+ write (iout,*)"Fragment",j," list",(list_frag(k,j),
+ & k=1,nlist_frag(j))
+ enddo
+ return
+ end
--- /dev/null
+ subroutine read_ref_structure(*)
+C
+C Read the reference structure from the PDB file or from a PDB file or in the form of the dihedral
+C angles.
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.NAMES'
+ include 'COMMON.CHAIN'
+ include 'COMMON.FFIELD'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.HEADER'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CONTACTS1'
+ include 'COMMON.PEPTCONT'
+ include 'COMMON.TIME1'
+ include 'COMMON.COMPAR'
+ character*4 sequence(maxres)
+ integer rescode
+ double precision x(maxvar)
+ integer itype_pdb(maxres)
+ logical seq_comp
+ integer i,j,k,nres_pdb,iaux
+ double precision ddsc,dist
+ integer ilen
+ external ilen
+C
+ nres0=nres
+ write (iout,*) "pdbref",pdbref
+ if (pdbref) then
+ read(inp,'(a)') pdbfile
+ write (iout,'(2a,1h.)') 'PDB data will be read from file ',
+ & pdbfile(:ilen(pdbfile))
+ open(ipdbin,file=pdbfile,status='old',err=33)
+ goto 34
+ 33 write (iout,'(a)') 'Error opening PDB file.'
+ return1
+ 34 continue
+ do i=1,nres
+ itype_pdb(i)=itype(i)
+ enddo
+ call readpdb(.true.)
+ do i=1,nres
+ iaux=itype_pdb(i)
+ itype_pdb(i)=itype(i)
+ itype(i)=iaux
+ enddo
+ close (ipdbin)
+ nres_pdb=nres
+ nres=nres0
+ nstart_seq=nnt
+ if (nsup.le.(nct-nnt+1)) then
+ do i=0,nct-nnt+1-nsup
+ if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),
+ & nsup)) then
+ do j=nnt+nsup-1,nnt,-1
+ do k=1,3
+ cref(k,nres+j+i)=cref(k,nres_pdb+j)
+ enddo
+ enddo
+ do j=nnt+nsup-1,nnt,-1
+ do k=1,3
+ cref(k,j+i)=cref(k,j)
+ enddo
+ phi_ref(j+i)=phi_ref(j)
+ theta_ref(j+i)=theta_ref(j)
+ alph_ref(j+i)=alph_ref(j)
+ omeg_ref(j+i)=omeg_ref(j)
+ enddo
+#ifdef DEBUG
+ do j=nnt,nct
+ write (iout,'(i5,3f10.5,5x,3f10.5)')
+ & j,(cref(k,j),k=1,3),(cref(k,j+nres),k=1,3)
+ enddo
+#endif
+ nstart_seq=nnt+i
+ nstart_sup=nnt+i
+ goto 111
+ endif
+ enddo
+ write (iout,'(a)')
+ & 'Error - sequences to be superposed do not match.'
+ return1
+ else
+ do i=0,nsup-(nct-nnt+1)
+ if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),
+ & nct-nnt+1))
+ & then
+ nstart_sup=nstart_sup+i
+ nsup=nct-nnt+1
+ goto 111
+ endif
+ enddo
+ write (iout,'(a)')
+ & 'Error - sequences to be superposed do not match.'
+ endif
+ 111 continue
+ write (iout,'(a,i5)')
+ & 'Experimental structure begins at residue',nstart_seq
+ else
+ call read_angles(inp,*38)
+ goto 39
+ 38 write (iout,'(a)') 'Error reading reference structure.'
+ return1
+ 39 call chainbuild
+ nstart_sup=nnt
+ nstart_seq=nnt
+ nsup=nct-nnt+1
+ do i=1,2*nres
+ do j=1,3
+ cref(j,i)=c(j,i)
+ enddo
+ enddo
+ endif
+ nend_sup=nstart_sup+nsup-1
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=cref(j,i)
+ enddo
+ enddo
+ do i=1,nres
+ do j=1,3
+ dc(j,nres+i)=cref(j,nres+i)-cref(j,i)
+ enddo
+ if (itype(i).ne.10) then
+ ddsc = dist(i,nres+i)
+ do j=1,3
+ dc_norm(j,nres+i)=dc(j,nres+i)/ddsc
+ enddo
+ else
+ do j=1,3
+ dc_norm(j,nres+i)=0.0d0
+ enddo
+ endif
+c write (iout,*) "i",i," dc_norm",(dc_norm(k,nres+i),k=1,3),
+c " norm",dc_norm(1,nres+i)**2+dc_norm(2,nres+i)**2+
+c dc_norm(3,nres+i)**2
+ do j=1,3
+ dc(j,i)=c(j,i+1)-c(j,i)
+ enddo
+ ddsc = dist(i,i+1)
+ do j=1,3
+ dc_norm(j,i)=dc(j,i)/ddsc
+ enddo
+ enddo
+c print *,"Calling contact"
+ call contact(.true.,ncont_ref,icont_ref(1,1),
+ & nstart_sup,nend_sup)
+c print *,"Calling elecont"
+ call elecont(.true.,ncont_pept_ref,
+ & icont_pept_ref(1,1),
+ & nstart_sup,nend_sup)
+ write (iout,'(a,i3,a,i3,a,i3,a)')
+ & 'Number of residues to be superposed:',nsup,
+ & ' (from residue',nstart_sup,' to residue',
+ & nend_sup,').'
+ return
+ end
--- /dev/null
+ subroutine readpdb
+C Read the PDB file and convert the peptide geometry into virtual-chain
+C geometry.
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ character*3 seq,atom,res
+ character*80 card
+ double precision sccor(3,20)
+ integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
+ double precision dcj
+ integer rescode
+ ibeg=1
+ ishift1=0
+ do i=1,10000
+ read (ipdbin,'(a80)',end=10) card
+ if (card(:3).eq.'END' .or. card(:3).eq.'TER') goto 10
+C Fish out the ATOM cards.
+ if (index(card(1:4),'ATOM').gt.0) then
+ read (card(14:16),'(a3)') atom
+ if (atom.eq.'CA' .or. atom.eq.'CH3') then
+C Calculate the CM of the preceding residue.
+ if (ibeg.eq.0) call sccenter(ires,iii,sccor)
+C Start new residue.
+ ires_old=ires+ishift-ishift1
+ read (card(23:26),*) ires
+c print *,"ires_old",ires_old," ires",ires
+ if (card(27:27).eq."A" .or. card(27:27).eq."B") then
+c ishift1=ishift1+1
+ endif
+ read (card(18:20),'(a3)') res
+ if (ibeg.eq.1) then
+ ishift=ires-1
+ if (res.ne.'GLY' .and. res.ne. 'ACE') then
+ ishift=ishift-1
+ itype(1)=21
+ endif
+ ibeg=0
+ else
+ ishift=ishift+ires-ires_old-1
+ endif
+ ires=ires-ishift+ishift1
+ if (res.eq.'ACE') then
+ ity=10
+ else
+ itype(ires)=rescode(ires,res,0)
+ endif
+ read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
+ write (iout,'(2i3,2x,a,3f8.3)')
+ & ires,itype(ires),res,(c(j,ires),j=1,3)
+ iii=1
+ do j=1,3
+ sccor(j,iii)=c(j,ires)
+ enddo
+c write (*,*) card(23:27),ires,itype(ires)
+ else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
+ & atom.ne.'N ' .and. atom.ne.'C ') then
+ iii=iii+1
+ read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
+ endif
+ endif
+ enddo
+ 10 write (iout,'(a,i5)') ' Nres: ',ires
+C Calculate the CM of the last side chain.
+ call sccenter(ires,iii,sccor)
+ nres=ires
+ nsup=nres
+ nstart_sup=1
+ if (itype(nres).ne.10) then
+ nres=nres+1
+ itype(nres)=21
+ do j=1,3
+ dcj=c(j,nres-2)-c(j,nres-3)
+ c(j,nres)=c(j,nres-1)+dcj
+ c(j,2*nres)=c(j,nres)
+ enddo
+ endif
+ do i=2,nres-1
+ do j=1,3
+ c(j,i+nres)=dc(j,i)
+ enddo
+ enddo
+ do j=1,3
+ c(j,nres+1)=c(j,1)
+ c(j,2*nres)=c(j,nres)
+ enddo
+ if (itype(1).eq.21) then
+ nsup=nsup-1
+ nstart_sup=2
+ do j=1,3
+ dcj=c(j,4)-c(j,3)
+ c(j,1)=c(j,2)-dcj
+ c(j,nres+1)=c(j,1)
+ enddo
+ endif
+C Copy the coordinates to reference coordinates
+ do i=1,2*nres
+ do j=1,3
+ cref(j,i)=c(j,i)
+ enddo
+ enddo
+C Calculate internal coordinates.
+ do ires=1,nres
+ write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
+ & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
+ & (c(j,ires+nres),j=1,3)
+ enddo
+ call flush(iout)
+ call int_from_cart(.true.,.true.)
+ do i=1,nres
+ phi_ref(i)=phi(i)
+ theta_ref(i)=theta(i)
+ alph_ref(i)=alph(i)
+ omeg_ref(i)=omeg(i)
+ enddo
+ ishift_pdb=ishift
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine int_from_cart(lside,lprn)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.LOCAL'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.NAMES'
+ character*3 seq,atom,res
+ character*80 card
+ double precision sccor(3,20)
+ integer rescode
+ double precision dist,alpha,beta,di
+ integer i,j,iti
+ logical lside,lprn
+ if (lprn) then
+ write (iout,'(/a)')
+ & 'Internal coordinates calculated from crystal structure.'
+ if (lside) then
+ write (iout,'(8a)') ' Res ',' dvb',' Theta',
+ & ' Phi',' Dsc_id',' Dsc',' Alpha',
+ & ' Omega'
+ else
+ write (iout,'(4a)') ' Res ',' dvb',' Theta',
+ & ' Phi'
+ endif
+ endif
+ do i=2,nres
+ iti=itype(i)
+ write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1)
+ if (itype(i-1).ne.21 .and. itype(i).ne.21 .and.
+ & (dist(i,i-1).lt.2.0D0 .or. dist(i,i-1).gt.5.0D0)) then
+ write (iout,'(a,i4)') 'Bad Cartesians for residue',i
+ stop
+ endif
+ theta(i+1)=alpha(i-1,i,i+1)
+ if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+ enddo
+ if (itype(1).eq.21) then
+ do j=1,3
+ c(j,1)=c(j,2)+(c(j,3)-c(j,4))
+ enddo
+ endif
+ if (itype(nres).eq.21) then
+ do j=1,3
+ c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
+ enddo
+ endif
+ if (lside) then
+ do i=2,nres-1
+ do j=1,3
+ c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
+ enddo
+ iti=itype(i)
+ di=dist(i,nres+i)
+ if (iti.ne.10) then
+ alph(i)=alpha(nres+i,i,maxres2)
+ omeg(i)=beta(nres+i,i,maxres2,i+1)
+ endif
+ if (lprn)
+ & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
+ & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
+ & rad2deg*alph(i),rad2deg*omeg(i)
+ enddo
+ else if (lprn) then
+ do i=2,nres
+ iti=itype(i)
+ write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
+ & rad2deg*theta(i),rad2deg*phi(i)
+ enddo
+ endif
+ return
+ end
+c---------------------------------------------------------------------------
+ subroutine sccenter(ires,nscat,sccor)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ integer ires,nscat,i,j
+ double precision sccor(3,20),sccmj
+ do j=1,3
+ sccmj=0.0D0
+ do i=1,nscat
+ sccmj=sccmj+sccor(j,i)
+ enddo
+ dc(j,ires)=sccmj/nscat
+ enddo
+ return
+ end
--- /dev/null
+ subroutine read_general_data(*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "COMMON.TORSION"
+ include "COMMON.INTERACT"
+ include "COMMON.IOUNITS"
+ include "COMMON.TIME1"
+ include "COMMON.PROT"
+ include "COMMON.PROTFILES"
+ include "COMMON.CHAIN"
+ include "COMMON.NAMES"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.WEIGHTS"
+ include "COMMON.FREE"
+ include "COMMON.CONTROL"
+ include "COMMON.ENERGIES"
+ character*800 controlcard
+ integer i,j,k,ii,n_ene_found
+ integer ind,itype1,itype2,itypf,itypsc,itypp
+ integer ilen
+ external ilen
+ character*16 ucase
+ character*16 key
+ external ucase
+
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,"N_ENE",n_ene,max_ene)
+ if (n_ene.gt.max_ene) then
+ write (iout,*) "Error: parameter out of range: N_ENE",n_ene,
+ & max_ene
+ return1
+ endif
+ call readi(controlcard,"NPARMSET",nparmset,1)
+ separate_parset = index(controlcard,"SEPARATE_PARSET").gt.0
+ call readi(controlcard,"IPARMPRINT",iparmprint,1)
+ write (iout,*) "PARMPRINT",iparmprint
+ if (nparmset.gt.max_parm) then
+ write (iout,*) "Error: parameter out of range: NPARMSET",
+ & nparmset, Max_Parm
+ return1
+ endif
+ energy_dec=index(controlcard,"ENERGY_DEC").gt.0
+ call readi(controlcard,"MAXIT",maxit,5000)
+ call reada(controlcard,"FIMIN",fimin,1.0d-3)
+ call readi(controlcard,"ENSEMBLES",ensembles,0)
+ hamil_rep=index(controlcard,"HAMIL_REP").gt.0
+ write (iout,*) "Number of energy parameter sets",nparmset
+ call multreadi(controlcard,"ISAMPL",isampl,nparmset,1)
+ write (iout,*) "MaxSlice",MaxSlice
+ call readi(controlcard,"NSLICE",nslice,1)
+ call flush(iout)
+ if (nslice.gt.MaxSlice) then
+ write (iout,*) "Error: parameter out of range: NSLICE",nslice,
+ & MaxSlice
+ return1
+ endif
+ write (iout,*) "Frequency of storing conformations",
+ & (isampl(i),i=1,nparmset)
+ write (iout,*) "Maxit",maxit," Fimin",fimin
+ call readi(controlcard,"NQ",nQ,1)
+ if (nQ.gt.MaxQ) then
+ write (iout,*) "Error: parameter out of range: NQ",nq,
+ & maxq
+ return1
+ endif
+ indpdb=0
+ if (index(controlcard,"CLASSIFY").gt.0) indpdb=1
+ call reada(controlcard,"DELTA",delta,1.0d-2)
+ call readi(controlcard,"EINICHECK",einicheck,2)
+ call reada(controlcard,"DELTRMS",deltrms,5.0d-2)
+ call readi(controlcard,"NGRIDT",NGridT,400)
+ call reada(controlcard,"STARTGRIDT",StartGridT,200.0d0)
+ call reada(controlcard,"DELTA_T",Delta_T,1.0d0)
+ call reada(controlcard,"DELTRGY",deltrgy,5.0d-2)
+ call readi(controlcard,"RESCALE",rescale_mode,1)
+ check_conf=index(controlcard,"NO_CHECK_CONF").eq.0
+ write (iout,*) "delta",delta
+ write (iout,*) "einicheck",einicheck
+ write (iout,*) "rescale_mode",rescale_mode
+ call flush(iout)
+ bxfile=index(controlcard,"BXFILE").gt.0
+ cxfile=index(controlcard,"CXFILE").gt.0
+ if (nslice .eq. 1 .and. .not.bxfile .and. .not.cxfile)
+ & bxfile=.true.
+ histfile=index(controlcard,"HISTFILE").gt.0
+ histout=index(controlcard,"HISTOUT").gt.0
+ entfile=index(controlcard,"ENTFILE").gt.0
+ zscfile=index(controlcard,"ZSCFILE").gt.0
+ with_dihed_constr = index(controlcard,"WITH_DIHED_CONSTR").gt.0
+ call readi(controlcard,'CONSTR_DIST',constr_dist,0)
+ write (iout,*) "with_dihed_constr ",with_dihed_constr,
+ & " CONSTR_DIST",constr_dist
+ refstr = index(controlcard,'REFSTR').gt.0
+ pdbref = index(controlcard,'PDBREF').gt.0
+ call flush(iout)
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine read_efree(*)
+C
+C Read molecular data
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.GEO'
+ include 'COMMON.FREE'
+ character*320 controlcard,ucase
+ integer iparm,ib,i,j,npars
+ integer ilen
+ external ilen
+
+ if (hamil_rep) then
+ npars=1
+ else
+ npars=nParmSet
+ endif
+
+ do iparm=1,npars
+
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'NT',nT_h(iparm),1)
+ write (iout,*) "iparm",iparm," nt",nT_h(iparm)
+ call flush(iout)
+ if (nT_h(iparm).gt.MaxT_h) then
+ write (iout,*) "Error: parameter out of range: NT",nT_h(iparm),
+ & MaxT_h
+ return1
+ endif
+ replica(iparm)=index(controlcard,"REPLICA").gt.0
+ umbrella(iparm)=index(controlcard,"UMBRELLA").gt.0
+ read_iset(iparm)=index(controlcard,"READ_ISET").gt.0
+ write (iout,*) "nQ",nQ," nT",nT_h(iparm)," replica ",
+ & replica(iparm)," umbrella ",umbrella(iparm),
+ & " read_iset",read_iset(iparm)
+ call flush(iout)
+ do ib=1,nT_h(iparm)
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'NR',nR(ib,iparm),1)
+ if (umbrella(iparm)) then
+ nRR(ib,iparm)=1
+ else
+ nRR(ib,iparm)=nR(ib,iparm)
+ endif
+ if (nR(ib,iparm).gt.MaxR) then
+ write (iout,*) "Error: parameter out of range: NR",
+ & nR(ib,iparm),MaxR
+ return1
+ endif
+ call reada(controlcard,'TEMP',beta_h(ib,iparm),298.0d0)
+ beta_h(ib,iparm)=1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ call multreada(controlcard,'FI',f(1,ib,iparm),nR(ib,iparm),
+ & 0.0d0)
+ do i=1,nR(ib,iparm)
+ call card_concat(controlcard,.true.)
+ call multreada(controlcard,'KH',KH(1,i,ib,iparm),nQ,
+ & 100.0d0)
+ call multreada(controlcard,'Q0',Q0(1,i,ib,iparm),nQ,
+ & 0.0d0)
+ enddo
+ enddo
+ do ib=1,nT_h(iparm)
+ write (iout,*) "ib",ib," beta_h",
+ & 1.0d0/(0.001987*beta_h(ib,iparm))
+ write (iout,*) "nR",nR(ib,iparm)
+ write (iout,*) "fi",(f(i,ib,iparm),i=1,nR(ib,iparm))
+ do i=1,nR(ib,iparm)
+ write (iout,*) "i",i," Kh",(Kh(j,i,ib,iparm),j=1,nQ),
+ & "q0",(q0(j,i,ib,iparm),j=1,nQ)
+ enddo
+ call flush(iout)
+ enddo
+
+ enddo
+
+ if (hamil_rep) then
+
+ do iparm=2,nParmSet
+ nT_h(iparm)=nT_h(1)
+ do ib=1,nT_h(iparm)
+ nR(ib,iparm)=nR(ib,1)
+ if (umbrella(iparm)) then
+ nRR(ib,iparm)=1
+ else
+ nRR(ib,iparm)=nR(ib,1)
+ endif
+ beta_h(ib,iparm)=beta_h(ib,1)
+ do i=1,nR(ib,iparm)
+ f(i,ib,iparm)=f(i,ib,1)
+ do j=1,nQ
+ KH(j,i,ib,iparm)=KH(j,i,ib,1)
+ Q0(j,i,ib,iparm)=Q0(j,i,ib,1)
+ enddo
+ enddo
+ replica(iparm)=replica(1)
+ umbrella(iparm)=umbrella(1)
+ read_iset(iparm)=read_iset(1)
+ enddo
+ enddo
+
+ endif
+
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine read_protein_data(*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROT"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.FREE"
+ include "COMMON.OBCINKA"
+ character*64 nazwa
+ character*16000 controlcard
+ integer i,ii,ib,iR,iparm,ilen,iroof,nthr,npars
+ external ilen,iroof
+ if (hamil_rep) then
+ npars=1
+ else
+ npars=nparmset
+ endif
+
+ do iparm=1,npars
+
+C Read names of files with conformation data.
+ if (replica(iparm)) then
+ nthr = 1
+ else
+ nthr = nT_h(iparm)
+ endif
+ do ib=1,nthr
+ do ii=1,nRR(ib,iparm)
+ write (iout,*) "Parameter set",iparm," temperature",ib,
+ & " window",ii
+ call flush(iout)
+ call card_concat(controlcard,.true.)
+ write (iout,*) controlcard(:ilen(controlcard))
+ call readi(controlcard,"NFILE_BIN",nfile_bin(ii,ib,iparm),0)
+ call readi(controlcard,"NFILE_ASC",nfile_asc(ii,ib,iparm),0)
+ call readi(controlcard,"NFILE_CX",nfile_cx(ii,ib,iparm),0)
+ call readi(controlcard,"REC_START",rec_start(ii,ib,iparm),1)
+ call readi(controlcard,"REC_END",rec_end(ii,ib,iparm),
+ & maxstr*isampl(iparm)+rec_start(ii,ib,iparm)-1)
+ call reada(controlcard,"TIME_START",
+ & time_start_collect(ii,ib,iparm),0.0d0)
+ call reada(controlcard,"TIME_END",time_end_collect(ii,ib,iparm),
+ & 1.0d10)
+ write (iout,*) "rec_start",rec_start(ii,ib,iparm),
+ & " rec_end",rec_end(ii,ib,iparm)
+ write (iout,*) "time_start",time_start_collect(ii,ib,iparm),
+ & " time_end",time_end_collect(ii,ib,iparm)
+ call flush(iout)
+ if (replica(iparm)) then
+ call readi(controlcard,"TOTRAJ",totraj(ii,iparm),1)
+ write (iout,*) "Number of trajectories",totraj(ii,iparm)
+ call flush(iout)
+ endif
+ if (nfile_bin(ii,ib,iparm).lt.2
+ & .and. nfile_asc(ii,ib,iparm).eq.0
+ & .and. nfile_cx(ii,ib,iparm).eq.0) then
+ write (iout,*) "Error - no action specified!"
+ return1
+ endif
+ if (nfile_bin(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,1,ii,ib,iparm),
+ & maxfile_prot,nfile_bin(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*)"nfile_bin",nfile_bin(ii,ib,iparm)
+ write(iout,*) (protfiles(i,1,ii,ib,iparm),
+ & i=1,nfile_bin(ii,ib,iparm))
+#endif
+ endif
+ if (nfile_asc(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,2,ii,ib,iparm),
+ & maxfile_prot,nfile_asc(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*) "nfile_asc(ii,ib,iparm)",nfile_asc(ii,ib,iparm)
+ write(iout,*) (protfiles(i,2,ii,ib,iparm),
+ & i=1,nfile_asc(ii,ib,iparm))
+#endif
+ else if (nfile_cx(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,2,ii,ib,iparm),
+ & maxfile_prot,nfile_cx(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*) "nfile_cx(ii,ib,iparm)",nfile_cx(ii,ib,iparm)
+ write(iout,*) (protfiles(i,2,ii,ib,iparm),
+ & i=1,nfile_cx(ii,ib,iparm))
+#endif
+ endif
+ call flush(iout)
+ enddo
+ enddo
+
+ enddo
+
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine opentmp(islice,iunit,bprotfile_temp)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.PROT"
+ include "COMMON.FREE"
+ character*64 bprotfile_temp
+ character*3 liczba,liczba2
+ character*2 liczba1
+ integer iunit,islice
+ integer ilen,iroof
+ external ilen,iroof
+ logical lerr
+
+ write (liczba1,'(bz,i2.2)') islice
+ write (liczba,'(bz,i3.3)') me
+#ifdef MPI
+c write (iout,*) "separate_parset ",separate_parset,
+c & " myparm",myparm
+ if (separate_parset) then
+ write (liczba2,'(bz,i3.3)') myparm
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//"_"//liczba2//".xbin.tmp"//liczba1
+ open (iunit,file=bprotfile_temp,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec)
+ else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"//liczba1
+ open (iunit,file=bprotfile_temp,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec)
+ endif
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"//liczba1
+ open (iunit,file=bprotfile_temp,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec)
+#endif
+c write (iout,*) "OpenTmp iunit",iunit," bprotfile_temp",
+c & bprotfile_temp
+c call flush(iout)
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine read_database(*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.GEO"
+ include "COMMON.ENEPS"
+ include "COMMON.PROT"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.SBRIDGE"
+ include "COMMON.OBCINKA"
+ real*4 csingle(3,maxres2)
+ character*64 nazwa,bprotfile_temp
+ character*3 liczba
+ character*2 liczba1
+ integer i,j,ii,jj(maxslice),k,kk(maxslice),l,
+ & ll(maxslice),mm(maxslice),if
+ integer nrec,nlines,iscor,iunit,islice
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ double precision rmsdev,energia(0:max_ene),efree,eini,temp
+ double precision prop(maxQ)
+ integer ntot_all(maxslice,0:maxprocs-1)
+ integer iparm,ib,iib,ir,nprop,nthr,npars
+ double precision etot,time
+ integer ixdrf,iret
+ logical lerr,linit
+
+ lenrec1=12*(nres+nct-nnt+1)+4*(2*nss+2)+24
+ lenrec2=12*(nres+nct-nnt+1)+4*(2*nss+2)+24+8*nQ
+ lenrec=lenrec2+8
+ write (iout,*) "lenrec",lenrec," lenrec1",lenrec1,
+ & " lenrec2",lenrec2
+
+ do i=1,nQ
+ prop(i)=0.0d0
+ enddo
+ do islice=1,nslice
+ ll(islice)=0
+ mm(islice)=0
+ enddo
+ write (iout,*) "nparmset",nparmset
+ if (hamil_rep) then
+ npars=1
+ else
+ npars=nparmset
+ endif
+ do iparm=1,npars
+
+ if (replica(iparm)) then
+ nthr = 1
+ else
+ nthr = nT_h(iparm)
+ endif
+
+ do ib=1,nthr
+ do iR=1,nRR(ib,iparm)
+
+ write (iout,*) "iparm",iparm," ib",ib," iR",iR," nQ",nQ
+ do islice=1,nslice
+ jj(islice)=0
+ kk(islice)=0
+ enddo
+
+ IF (NFILE_BIN(iR,ib,iparm).GT.0) THEN
+c Read conformations from binary DA files (one per batch) and write them to
+c a binary DA scratchfile.
+ write (liczba,'(bz,i3.3)') me
+ do if=1,nfile_bin(iR,ib,iparm)
+ nazwa=protfiles(if,1,iR,ib,iparm)
+ & (:ilen(protfiles(if,1,iR,ib,iparm)))//".bx"
+ open (ientin,file=nazwa,status="old",form="unformatted",
+ & access="direct",recl=lenrec2,err=1111)
+ ii=0
+ do islice=1,nslice
+ call opentmp(islice,ientout,bprotfile_temp)
+ call bxread(nazwa,ii,jj(islice),kk(islice),ll(islice),
+ & mm(islice),iR,ib,iparm)
+ close(ientout)
+ enddo
+ close(ientin)
+ enddo
+ ENDIF ! NFILE_BIN>0
+c
+ IF (NFILE_ASC(iR,ib,iparm).GT.0) THEN
+c Read conformations from multiple ASCII int files and write them to a binary
+c DA scratchfile.
+ do if=1,nfile_asc(iR,ib,iparm)
+ nazwa=protfiles(if,2,iR,ib,iparm)
+ & (:ilen(protfiles(if,2,iR,ib,iparm)))//".x"
+ open(unit=ientin,file=nazwa,status='old',err=1111)
+ write(iout,*) "reading ",nazwa(:ilen(nazwa))
+ ii=0
+ call xread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm)
+ enddo ! if
+ ENDIF
+ IF (NFILE_CX(iR,ib,iparm).gt.0) THEN
+c Read conformations from cx files and write them to a binary
+c DA scratchfile.
+ do if=1,nfile_cx(iR,ib,iparm)
+ nazwa=protfiles(if,2,iR,ib,iparm)
+ & (:ilen(protfiles(if,2,iR,ib,iparm)))//".cx"
+ write(iout,*) "reading ",nazwa(:ilen(nazwa))
+ ii=0
+ print *,"Calling cxread"
+ call cxread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm,
+ & *1111)
+ close(ientout)
+ write (iout,*) "exit cxread"
+ call flush(iout)
+ enddo
+ ENDIF
+
+ do islice=1,nslice
+ stot(islice)=stot(islice)+jj(islice)
+ enddo
+
+ enddo
+ enddo
+ write (iout,*) "IPARM",iparm
+ enddo
+
+ if (nslice.eq.1) then
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"
+#endif
+ write(iout,*) mm(1)," conformations read",ll(1),
+ & " conformations written to ",
+ & bprotfile_temp(:ilen(bprotfile_temp))
+ else
+ do islice=1,nslice
+ write (liczba1,'(bz,i2.2)') islice
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"//liczba1
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"//liczba1
+#endif
+ write(iout,*) mm(islice)," conformations read",ll(islice),
+ & " conformations written to ",
+ & bprotfile_temp(:ilen(bprotfile_temp))
+ enddo
+ endif
+
+#ifdef MPI
+c Check if everyone has the same number of conformations
+ call MPI_Allgather(stot(1),maxslice,MPI_INTEGER,
+ & ntot_all(1,0),maxslice,MPI_INTEGER,MPI_Comm_World,IERROR)
+ lerr=.false.
+ do i=0,nprocs-1
+ if (i.ne.me) then
+ do islice=1,nslice
+ if (stot(islice).ne.ntot_all(islice,i)) then
+ write (iout,*) "Number of conformations at processor",i,
+ & " differs from that at processor",me,
+ & stot(islice),ntot_all(islice,i)," slice",islice
+ lerr = .true.
+ endif
+ enddo
+ endif
+ enddo
+ if (lerr) then
+ write (iout,*)
+ write (iout,*) "Numbers of conformations read by processors"
+ write (iout,*)
+ do i=0,nprocs-1
+ write (iout,'(8i10)') i,(ntot_all(islice,i),islice=1,nslice)
+ enddo
+ write (iout,*) "Calculation terminated."
+ call flush(iout)
+ return1
+ endif
+ do islice=1,nslice
+ ntot(islice)=stot(islice)
+ enddo
+ return
+#endif
+ 1111 write(iout,*) "Error opening coordinate file ",nazwa(:ilen(nazwa))
+ call flush(iout)
+ return1
+ end
+c------------------------------------------------------------------------------
+ subroutine card_concat(card,to_upper)
+ implicit none
+ include 'DIMENSIONS.ZSCOPT'
+ include "COMMON.IOUNITS"
+ character*(*) card
+ character*80 karta,ucase
+ logical to_upper
+ integer ilen
+ external ilen
+ read (inp,'(a)') karta
+ if (to_upper) karta=ucase(karta)
+ card=' '
+ do while (karta(80:80).eq.'&')
+ card=card(:ilen(card)+1)//karta(:79)
+ read (inp,'(a)') karta
+ if (to_upper) karta=ucase(karta)
+ enddo
+ card=card(:ilen(card)+1)//karta
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine readi(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch
+ integer wartosc,default
+ integer ilen,iread
+ external ilen
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*) wartosc
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine reada(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch
+ character*80 aux
+ double precision wartosc,default
+ integer ilen,iread
+ external ilen
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*) wartosc
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreadi(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ integer tablica(dim),default
+ character*(*) rekord,lancuch
+ character*80 aux
+ integer ilen,iread
+ external ilen
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) return
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
+ 10 return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreada(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ double precision tablica(dim),default
+ character*(*) rekord,lancuch
+ character*80 aux
+ integer ilen,iread
+ external ilen
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) return
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
+ 10 return
+ end
+c----------------------------------------------------------------------------
+ subroutine reads(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch,wartosc,default
+ character*80 aux
+ integer ilen,lenlan,lenrec,iread,ireade
+ external ilen
+ logical iblnk
+ external iblnk
+ lenlan=ilen(lancuch)
+ lenrec=ilen(rekord)
+ iread=index(rekord,lancuch(:lenlan)//"=")
+c print *,"rekord",rekord," lancuch",lancuch
+c print *,"iread",iread," lenlan",lenlan," lenrec",lenrec
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+lenlan+1
+c print *,"iread",iread
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ do while (iread.le.lenrec .and. iblnk(rekord(iread:iread)))
+ iread=iread+1
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ enddo
+c print *,"iread",iread
+ if (iread.gt.lenrec) then
+ wartosc=default
+ return
+ endif
+ ireade=iread+1
+c print *,"ireade",ireade
+ do while (ireade.lt.lenrec .and.
+ & .not.iblnk(rekord(ireade:ireade)))
+ ireade=ireade+1
+ enddo
+ wartosc=rekord(iread:ireade)
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreads(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ character*(*) rekord,lancuch,tablica(dim),default
+ character*80 aux
+ integer ilen,lenlan,lenrec,iread,ireade
+ external ilen
+ logical iblnk
+ external iblnk
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ lenlan=ilen(lancuch)
+ lenrec=ilen(rekord)
+ iread=index(rekord,lancuch(:lenlan)//"=")
+c print *,"rekord",rekord," lancuch",lancuch
+c print *,"iread",iread," lenlan",lenlan," lenrec",lenrec
+ if (iread.eq.0) return
+ iread=iread+lenlan+1
+ do i=1,dim
+c print *,"iread",iread
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ do while (iread.le.lenrec .and. iblnk(rekord(iread:iread)))
+ iread=iread+1
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ enddo
+c print *,"iread",iread
+ if (iread.gt.lenrec) return
+ ireade=iread+1
+c print *,"ireade",ireade
+ do while (ireade.lt.lenrec .and.
+ & .not.iblnk(rekord(ireade:ireade)))
+ ireade=ireade+1
+ enddo
+ tablica(i)=rekord(iread:ireade)
+ iread=ireade+1
+ enddo
+ end
+c----------------------------------------------------------------------------
+ subroutine split_string(rekord,tablica,dim,nsub)
+ implicit none
+ integer dim,nsub,i,ii,ll,kk
+ character*(*) tablica(dim)
+ character*(*) rekord
+ integer ilen
+ external ilen
+ do i=1,dim
+ tablica(i)=" "
+ enddo
+ ii=1
+ ll = ilen(rekord)
+ nsub=0
+ do i=1,dim
+C Find the start of term name
+ kk = 0
+ do while (ii.le.ll .and. rekord(ii:ii).eq." ")
+ ii = ii+1
+ enddo
+C Parse the name into TABLICA(i) until blank found
+ do while (ii.le.ll .and. rekord(ii:ii).ne." ")
+ kk = kk+1
+ tablica(i)(kk:kk)=rekord(ii:ii)
+ ii = ii+1
+ enddo
+ if (kk.gt.0) nsub=nsub+1
+ if (ii.gt.ll) return
+ enddo
+ return
+ end
+c--------------------------------------------------------------------------------
+ integer function iroof(n,m)
+ ii = n/m
+ if (ii*m .lt. n) ii=ii+1
+ iroof = ii
+ return
+ end
--- /dev/null
+ subroutine read_general_data(*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "COMMON.TORSION"
+ include "COMMON.INTERACT"
+ include "COMMON.IOUNITS"
+ include "COMMON.TIME1"
+ include "COMMON.PROT"
+ include "COMMON.PROTFILES"
+ include "COMMON.CHAIN"
+ include "COMMON.NAMES"
+ include "COMMON.FFIELD"
+ include "COMMON.ENEPS"
+ include "COMMON.WEIGHTS"
+ include "COMMON.FREE"
+ include "COMMON.CONTROL"
+ include "COMMON.ENERGIES"
+ character*800 controlcard
+ integer i,j,k,ii,n_ene_found
+ integer ind,itype1,itype2,itypf,itypsc,itypp
+ integer ilen
+ external ilen
+ character*16 ucase
+ character*16 key
+ external ucase
+
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,"N_ENE",n_ene,max_ene)
+ if (n_ene.gt.max_ene) then
+ write (iout,*) "Error: parameter out of range: N_ENE",n_ene,
+ & max_ene
+ return1
+ endif
+ call readi(controlcard,"NPARMSET",nparmset,1)
+ if (nparmset.gt.max_parm) then
+ write (iout,*) "Error: parameter out of range: NPARMSET",
+ & nparmset, Max_Parm
+ return1
+ endif
+ call readi(controlcard,"MAXIT",maxit,5000)
+ call reada(controlcard,"FIMIN",fimin,1.0d-3)
+ call readi(controlcard,"ENSEMBLES",ensembles,0)
+ write (iout,*) "Number of energy parameter sets",nparmset
+ call multreadi(controlcard,"ISAMPL",isampl,nparmset,1)
+ write (iout,*) "MaxSlice",MaxSlice
+ call readi(controlcard,"NSLICE",nslice,1)
+ call flush(iout)
+ if (nslice.gt.MaxSlice) then
+ write (iout,*) "Error: parameter out of range: NSLICE",nslice,
+ & MaxSlice
+ return1
+ endif
+ write (iout,*) "Frequency of storing conformations",
+ & (isampl(i),i=1,nparmset)
+ write (iout,*) "Maxit",maxit," Fimin",fimin
+ call readi(controlcard,"NQ",nQ,1)
+ if (nQ.gt.MaxQ) then
+ write (iout,*) "Error: parameter out of range: NQ",nq,
+ & maxq
+ return1
+ endif
+ indpdb=0
+ if (index(controlcard,"CLASSIFY").gt.0) indpdb=1
+ call reada(controlcard,"DELTA",delta,1.0d-2)
+ call readi(controlcard,"EINICHECK",einicheck,2)
+ call reada(controlcard,"DELTRMS",deltrms,5.0d-2)
+ call reada(controlcard,"DELTRGY",deltrgy,5.0d-2)
+ call readi(controlcard,"RESCALE",rescale_mode,1)
+ write (iout,*) "delta",delta
+ write (iout,*) "einicheck",einicheck
+ write (iout,*) "rescale_mode",rescale_mode
+ call flush(iout)
+ bxfile=index(controlcard,"BXFILE").gt.0
+ cxfile=index(controlcard,"CXFILE").gt.0
+ if (nslice .eq. 1 .and. .not.bxfile .and. .not.cxfile)
+ & bxfile=.true.
+ histfile=index(controlcard,"HISTFILE").gt.0
+ entfile=index(controlcard,"ENTFILE").gt.0
+ zscfile=index(controlcard,"ZSCFILE").gt.0
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine read_efree(iparm,*)
+C
+C Read molecular data
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.GEO'
+ include 'COMMON.FREE'
+ character*320 controlcard,ucase
+ integer iparm,ib,i,j
+ integer ilen
+ external ilen
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'NT',nT_h(iparm),1)
+ if (nT_h(iparm).gt.MaxT_h) then
+ write (iout,*) "Error: parameter out of range: NT",nT_h(iparm),
+ & MaxT_h
+ return1
+ endif
+ replica(iparm)=index(controlcard,"REPLICA").gt.0
+ umbrella(iparm)=index(controlcard,"UMBRELLA").gt.0
+ read_iset(iparm)=index(controlcard,"READ_ISET").gt.0
+ write (iout,*) "nQ",nQ," nT",nT_h(iparm)," replica ",
+ & replica(iparm)," umbrella ",umbrella(iparm),
+ & " read_iset",read_iset(iparm)
+ call flush(iout)
+ do ib=1,nT_h(iparm)
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'NR',nR(ib,iparm),1)
+ if (umbrella(iparm)) then
+ nRR(ib,iparm)=1
+ else
+ nRR(ib,iparm)=nR(ib,iparm)
+ endif
+ if (nR(ib,iparm).gt.MaxR) then
+ write (iout,*) "Error: parameter out of range: NR",
+ & nR(ib,iparm),MaxR
+ return1
+ endif
+ call reada(controlcard,'TEMP',beta_h(ib,iparm),298.0d0)
+ beta_h(ib,iparm)=1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ call multreada(controlcard,'FI',f(1,ib,iparm),nR(ib,iparm),
+ & 0.0d0)
+ do i=1,nR(ib,iparm)
+ call card_concat(controlcard,.true.)
+ call multreada(controlcard,'KH',KH(1,i,ib,iparm),nQ,
+ & 100.0d0)
+ call multreada(controlcard,'Q0',Q0(1,i,ib,iparm),nQ,
+ & 0.0d0)
+ enddo
+ enddo
+ do ib=1,nT_h(iparm)
+ write (iout,*) "ib",ib," beta_h",
+ & 1.0d0/(0.001987*beta_h(ib,iparm))
+ write (iout,*) "nR",nR(ib,iparm)
+ write (iout,*) "fi",(f(i,ib,iparm),i=1,nR(ib,iparm))
+ do i=1,nR(ib,iparm)
+ write (iout,*) "i",i," Kh",(Kh(j,i,ib,iparm),j=1,nQ),
+ & "q0",(q0(j,i,ib,iparm),j=1,nQ)
+ enddo
+ call flush(iout)
+ enddo
+ return
+ end
+c-----------------------------------------------------------------------------
+ subroutine read_protein_data(iparm,*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROT"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.FREE"
+ include "COMMON.OBCINKA"
+ character*64 nazwa
+ character*16000 controlcard
+ integer i,ii,ib,iR,iparm,ilen,iroof,nthr
+ external ilen,iroof
+ call flush(iout)
+C Read names of files with conformation data.
+ if (replica(iparm)) then
+ nthr = 1
+ else
+ nthr = nT_h(iparm)
+ endif
+ do ib=1,nthr
+ do ii=1,nRR(ib,iparm)
+ write (iout,*) "Parameter set",iparm," temperature",ib,
+ & " window",ii
+ call card_concat(controlcard,.true.)
+ write (iout,*) controlcard(:ilen(controlcard))
+ call readi(controlcard,"NFILE_BIN",nfile_bin(ii,ib,iparm),0)
+ call readi(controlcard,"NFILE_ASC",nfile_asc(ii,ib,iparm),0)
+ call readi(controlcard,"NFILE_CX",nfile_cx(ii,ib,iparm),0)
+ call readi(controlcard,"REC_START",rec_start(ii,ib,iparm),1)
+ call readi(controlcard,"REC_END",rec_end(ii,ib,iparm),
+ & maxstr*isampl(iparm)+rec_start(ii,ib,iparm)-1)
+ call reada(controlcard,"TIME_START",
+ & time_start_collect(ii,ib,iparm),0.0d0)
+ call reada(controlcard,"TIME_END",time_end_collect(ii,ib,iparm),
+ & 1.0d10)
+ write (iout,*) "rec_start",rec_start(ii,ib,iparm),
+ & " rec_end",rec_end(ii,ib,iparm)
+ write (iout,*) "time_start",time_start_collect(ii,ib,iparm),
+ & " time_end",time_end_collect(ii,ib,iparm)
+ call flush(iout)
+ if (replica(iparm)) then
+ call readi(controlcard,"TOTRAJ",totraj(ii,iparm),1)
+ write (iout,*) "Number of trajectories",totraj(ii,iparm)
+ call flush(iout)
+ endif
+ if (nfile_bin(ii,ib,iparm).lt.2
+ & .and. nfile_asc(ii,ib,iparm).eq.0
+ & .and. nfile_cx(ii,ib,iparm).eq.0) then
+ write (iout,*) "Error - no action specified!"
+ return1
+ endif
+ if (nfile_bin(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,1,ii,ib,iparm),
+ & maxfile_prot,nfile_bin(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*)"nfile_bin",nfile_bin(ii,ib,iparm)
+ write(iout,*) (protfiles(i,1,ii,ib,iparm),
+ & i=1,nfile_bin(ii,ib,iparm))
+#endif
+ endif
+ if (nfile_asc(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,2,ii,ib,iparm),
+ & maxfile_prot,nfile_asc(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*) "nfile_asc(ii,ib,iparm)",nfile_asc(ii,ib,iparm)
+ write(iout,*) (protfiles(i,2,ii,ib,iparm),
+ & i=1,nfile_asc(ii,ib,iparm))
+#endif
+ else if (nfile_cx(ii,ib,iparm).gt.0) then
+ call card_concat(controlcard,.false.)
+ call split_string(controlcard,protfiles(1,2,ii,ib,iparm),
+ & maxfile_prot,nfile_cx(ii,ib,iparm))
+#ifdef DEBUG
+ write(iout,*) "nfile_cx(ii,ib,iparm)",nfile_cx(ii,ib,iparm)
+ write(iout,*) (protfiles(i,2,ii,ib,iparm),
+ & i=1,nfile_cx(ii,ib,iparm))
+#endif
+ endif
+ call flush(iout)
+ enddo
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine opentmp(islice,iunit,bprotfile_temp)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.PROT"
+ character*64 bprotfile_temp
+ character*3 liczba
+ character*2 liczba1
+ integer iunit,islice
+ integer ilen,iroof
+ external ilen,iroof
+ logical lerr
+
+ write (liczba1,'(bz,i2.2)') islice
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"//liczba1
+ open (iunit,file=bprotfile_temp,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec)
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"//liczba1
+ open (iunit,file=bprotfile_temp,status="unknown",
+ & form="unformatted",access="direct",recl=lenrec)
+#endif
+ return
+ end
+c-------------------------------------------------------------------------------
+ subroutine read_database(*)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.GEO"
+ include "COMMON.ENEPS"
+ include "COMMON.PROT"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.SBRIDGE"
+ include "COMMON.OBCINKA"
+ real*4 csingle(3,maxres2)
+ character*64 nazwa,bprotfile_temp
+ character*3 liczba
+ character*2 liczba1
+ integer i,j,ii,jj(maxslice),k,kk(maxslice),l,
+ & ll(maxslice),mm(maxslice),if
+ integer nrec,nlines,iscor,iunit,islice
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ double precision rmsdev,energia(0:max_ene),efree,eini,temp
+ double precision prop(maxQ)
+ integer ntot_all(maxslice,0:maxprocs-1)
+ integer iparm,ib,iib,ir,nprop,nthr
+ double precision etot,time
+ integer ixdrf,iret
+ logical lerr,linit
+
+ lenrec1=12*(nres+nct-nnt+1)+4*(2*nss+2)+24
+ lenrec2=12*(nres+nct-nnt+1)+4*(2*nss+2)+24+8*nQ
+ lenrec=lenrec2+8
+ write (iout,*) "lenrec",lenrec," lenrec1",lenrec1,
+ & " lenrec2",lenrec2
+
+ do i=1,nQ
+ prop(i)=0.0d0
+ enddo
+ do islice=1,nslice
+ ll(islice)=0
+ mm(islice)=0
+ enddo
+ write (iout,*) "nparmset",nparmset
+ do iparm=1,nparmset
+
+ if (replica(iparm)) then
+ nthr = 1
+ else
+ nthr = nT_h(iparm)
+ endif
+
+ do ib=1,nthr
+ do iR=1,nRR(ib,iparm)
+
+ write (iout,*) "iparm",iparm," ib",ib," iR",iR," nQ",nQ
+ do islice=1,nslice
+ jj(islice)=0
+ kk(islice)=0
+ enddo
+
+ IF (NFILE_BIN(iR,ib,iparm).GT.0) THEN
+c Read conformations from binary DA files (one per batch) and write them to
+c a binary DA scratchfile.
+ write (liczba,'(bz,i3.3)') me
+ do if=1,nfile_bin(iR,ib,iparm)
+ nazwa=protfiles(if,1,iR,ib,iparm)
+ & (:ilen(protfiles(if,1,iR,ib,iparm)))//".bx"
+ open (ientin,file=nazwa,status="old",form="unformatted",
+ & access="direct",recl=lenrec2,err=1111)
+ ii=0
+ do islice=1,nslice
+ call opentmp(islice,ientout,bprotfile_temp)
+ call bxread(nazwa,ii,jj(islice),kk(islice),ll(islice),
+ & mm(islice),iR,ib,iparm)
+ close(ientout)
+ enddo
+ close(ientin)
+ enddo
+ ENDIF ! NFILE_BIN>0
+c
+ IF (NFILE_ASC(iR,ib,iparm).GT.0) THEN
+c Read conformations from multiple ASCII int files and write them to a binary
+c DA scratchfile.
+ do if=1,nfile_asc(iR,ib,iparm)
+ nazwa=protfiles(if,2,iR,ib,iparm)
+ & (:ilen(protfiles(if,2,iR,ib,iparm)))//".x"
+ open(unit=ientin,file=nazwa,status='old',err=1111)
+ write(iout,*) "reading ",nazwa(:ilen(nazwa))
+ ii=0
+ call xread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm)
+ enddo ! if
+ ENDIF
+ IF (NFILE_CX(iR,ib,iparm).gt.0) THEN
+c Read conformations from cx files and write them to a binary
+c DA scratchfile.
+ do if=1,nfile_cx(iR,ib,iparm)
+ nazwa=protfiles(if,2,iR,ib,iparm)
+ & (:ilen(protfiles(if,2,iR,ib,iparm)))//".cx"
+ write(iout,*) "reading ",nazwa(:ilen(nazwa))
+ ii=0
+ print *,"Calling cxread"
+ call cxread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm,
+ & *1111)
+ close(ientout)
+ write (iout,*) "exit cxread"
+ call flush(iout)
+ enddo
+ ENDIF
+
+ do islice=1,nslice
+ stot(islice)=stot(islice)+jj(islice)
+ enddo
+
+ enddo
+ enddo
+ write (iout,*) "IPARM",iparm
+ enddo
+
+ if (nslice.eq.1) then
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"
+#endif
+ write(iout,*) mm(1)," conformations read",ll(1),
+ & " conformations written to ",
+ & bprotfile_temp(:ilen(bprotfile_temp))
+ else
+ do islice=1,nslice
+ write (liczba1,'(bz,i2.2)') islice
+#ifdef MPI
+ write (liczba,'(bz,i3.3)') me
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//"/"//
+ & prefix(:ilen(prefix))//liczba//".xbin.tmp"//liczba1
+#else
+ bprotfile_temp = scratchdir(:ilen(scratchdir))//
+ & "/"//prefix(:ilen(prefix))//".xbin.tmp"//liczba1
+#endif
+ write(iout,*) mm(islice)," conformations read",ll(islice),
+ & " conformations written to ",
+ & bprotfile_temp(:ilen(bprotfile_temp))
+ enddo
+ endif
+
+#ifdef MPI
+c Check if everyone has the same number of conformations
+ call MPI_Allgather(stot(1),maxslice,MPI_INTEGER,
+ & ntot_all(1,0),maxslice,MPI_INTEGER,MPI_Comm_World,IERROR)
+ lerr=.false.
+ do i=0,nprocs-1
+ if (i.ne.me) then
+ do islice=1,nslice
+ if (stot(islice).ne.ntot_all(islice,i)) then
+ write (iout,*) "Number of conformations at processor",i,
+ & " differs from that at processor",me,
+ & stot(islice),ntot_all(islice,i)," slice",islice
+ lerr = .true.
+ endif
+ enddo
+ endif
+ enddo
+ if (lerr) then
+ write (iout,*)
+ write (iout,*) "Numbers of conformations read by processors"
+ write (iout,*)
+ do i=0,nprocs-1
+ write (iout,'(8i10)') i,(ntot_all(islice,i),islice=1,nslice)
+ enddo
+ write (iout,*) "Calculation terminated."
+ call flush(iout)
+ return1
+ endif
+ do islice=1,nslice
+ ntot(islice)=stot(islice)
+ enddo
+ return
+#endif
+ 1111 write(iout,*) "Error opening coordinate file ",nazwa(:ilen(nazwa))
+ call flush(iout)
+ return1
+ end
+c------------------------------------------------------------------------------
+ subroutine card_concat(card,to_upper)
+ implicit none
+ include 'DIMENSIONS.ZSCOPT'
+ include "COMMON.IOUNITS"
+ character*(*) card
+ character*80 karta,ucase
+ logical to_upper
+ integer ilen
+ external ilen
+ read (inp,'(a)') karta
+ if (to_upper) karta=ucase(karta)
+ card=' '
+ do while (karta(80:80).eq.'&')
+ card=card(:ilen(card)+1)//karta(:79)
+ read (inp,'(a)') karta
+ if (to_upper) karta=ucase(karta)
+ enddo
+ card=card(:ilen(card)+1)//karta
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine readi(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch
+ integer wartosc,default
+ integer ilen,iread
+ external ilen
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*) wartosc
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine reada(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch
+ character*80 aux
+ double precision wartosc,default
+ integer ilen,iread
+ external ilen
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*) wartosc
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreadi(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ integer tablica(dim),default
+ character*(*) rekord,lancuch
+ character*80 aux
+ integer ilen,iread
+ external ilen
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) return
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
+ 10 return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreada(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ double precision tablica(dim),default
+ character*(*) rekord,lancuch
+ character*80 aux
+ integer ilen,iread
+ external ilen
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ iread=index(rekord,lancuch(:ilen(lancuch))//"=")
+ if (iread.eq.0) return
+ iread=iread+ilen(lancuch)+1
+ read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
+ 10 return
+ end
+c----------------------------------------------------------------------------
+ subroutine reads(rekord,lancuch,wartosc,default)
+ implicit none
+ character*(*) rekord,lancuch,wartosc,default
+ character*80 aux
+ integer ilen,lenlan,lenrec,iread,ireade
+ external ilen
+ logical iblnk
+ external iblnk
+ lenlan=ilen(lancuch)
+ lenrec=ilen(rekord)
+ iread=index(rekord,lancuch(:lenlan)//"=")
+c print *,"rekord",rekord," lancuch",lancuch
+c print *,"iread",iread," lenlan",lenlan," lenrec",lenrec
+ if (iread.eq.0) then
+ wartosc=default
+ return
+ endif
+ iread=iread+lenlan+1
+c print *,"iread",iread
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ do while (iread.le.lenrec .and. iblnk(rekord(iread:iread)))
+ iread=iread+1
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ enddo
+c print *,"iread",iread
+ if (iread.gt.lenrec) then
+ wartosc=default
+ return
+ endif
+ ireade=iread+1
+c print *,"ireade",ireade
+ do while (ireade.lt.lenrec .and.
+ & .not.iblnk(rekord(ireade:ireade)))
+ ireade=ireade+1
+ enddo
+ wartosc=rekord(iread:ireade)
+ return
+ end
+c----------------------------------------------------------------------------
+ subroutine multreads(rekord,lancuch,tablica,dim,default)
+ implicit none
+ integer dim,i
+ character*(*) rekord,lancuch,tablica(dim),default
+ character*80 aux
+ integer ilen,lenlan,lenrec,iread,ireade
+ external ilen
+ logical iblnk
+ external iblnk
+ do i=1,dim
+ tablica(i)=default
+ enddo
+ lenlan=ilen(lancuch)
+ lenrec=ilen(rekord)
+ iread=index(rekord,lancuch(:lenlan)//"=")
+c print *,"rekord",rekord," lancuch",lancuch
+c print *,"iread",iread," lenlan",lenlan," lenrec",lenrec
+ if (iread.eq.0) return
+ iread=iread+lenlan+1
+ do i=1,dim
+c print *,"iread",iread
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ do while (iread.le.lenrec .and. iblnk(rekord(iread:iread)))
+ iread=iread+1
+c print *,"|",rekord(iread:iread),"|",iblnk(rekord(iread:iread))
+ enddo
+c print *,"iread",iread
+ if (iread.gt.lenrec) return
+ ireade=iread+1
+c print *,"ireade",ireade
+ do while (ireade.lt.lenrec .and.
+ & .not.iblnk(rekord(ireade:ireade)))
+ ireade=ireade+1
+ enddo
+ tablica(i)=rekord(iread:ireade)
+ iread=ireade+1
+ enddo
+ end
+c----------------------------------------------------------------------------
+ subroutine split_string(rekord,tablica,dim,nsub)
+ implicit none
+ integer dim,nsub,i,ii,ll,kk
+ character*(*) tablica(dim)
+ character*(*) rekord
+ integer ilen
+ external ilen
+ do i=1,dim
+ tablica(i)=" "
+ enddo
+ ii=1
+ ll = ilen(rekord)
+ nsub=0
+ do i=1,dim
+C Find the start of term name
+ kk = 0
+ do while (ii.le.ll .and. rekord(ii:ii).eq." ")
+ ii = ii+1
+ enddo
+C Parse the name into TABLICA(i) until blank found
+ do while (ii.le.ll .and. rekord(ii:ii).ne." ")
+ kk = kk+1
+ tablica(i)(kk:kk)=rekord(ii:ii)
+ ii = ii+1
+ enddo
+ if (kk.gt.0) nsub=nsub+1
+ if (ii.gt.ll) return
+ enddo
+ return
+ end
+c--------------------------------------------------------------------------------
+ integer function iroof(n,m)
+ ii = n/m
+ if (ii*m .lt. n) ii=ii+1
+ iroof = ii
+ return
+ end
--- /dev/null
+ subroutine read_compar
+C
+C Read molecular data
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.GEO'
+ include 'COMMON.FREE'
+ character*320 controlcard,ucase
+ character*64 wfile
+ integer ilen
+ external ilen
+ integer i,j,k
+
+ call card_concat(controlcard,.true.)
+ pdbref=(index(controlcard,'PDBREF').gt.0)
+ call reada(controlcard,'CUTOFF_UP',rmscut_base_up,4.0d0)
+ call reada(controlcard,'CUTOFF_LOW',rmscut_base_low,3.0d0)
+ call reada(controlcard,'RMSUP_LIM',rmsup_lim,4.0d0)
+ call reada(controlcard,'RMSUPUP_LIM',rmsupup_lim,7.5d0)
+ verbose = index(controlcard,"VERBOSE").gt.0
+ lgrp=index(controlcard,"STATIN").gt.0
+ lgrp_out=index(controlcard,"STATOUT").gt.0
+ merge_helices=index(controlcard,"DONT_MERGE_HELICES").eq.0
+ binary = index(controlcard,"BINARY").gt.0
+ rmscut_base_up=rmscut_base_up/50
+ rmscut_base_low=rmscut_base_low/50
+ call reada(controlcard,"FRAC_SEC",frac_sec,0.66666666d0)
+ call readi(controlcard,'NLEVEL',nlevel,1)
+ if (nlevel.lt.0) goto 121
+c Read the data pertaining to elementary fragments (level 1)
+ call readi(controlcard,'NFRAG',nfrag(1),0)
+ write(iout,*)"nfrag(1)",nfrag(1)
+ do j=1,nfrag(1)
+ call card_concat(controlcard,.true.)
+ write (iout,*) controlcard(:ilen(controlcard))
+ call readi(controlcard,'NPIECE',npiece(j,1),0)
+ call readi(controlcard,'N_SHIFT1',n_shift(1,j,1),0)
+ call readi(controlcard,'N_SHIFT2',n_shift(2,j,1),0)
+ call reada(controlcard,'ANGCUT',ang_cut(j),50.0d0)
+ call reada(controlcard,'MAXANG',ang_cut1(j),360.0d0)
+ call reada(controlcard,'FRAC_MIN',frac_min(j),0.666666d0)
+ call reada(controlcard,'NC_FRAC',nc_fragm(j,1),0.5d0)
+ call readi(controlcard,'NC_REQ',nc_req_setf(j,1),0)
+ call readi(controlcard,'RMS',irms(j,1),0)
+ call readi(controlcard,'LOCAL',iloc(j),1)
+ call readi(controlcard,'ELCONT',ielecont(j,1),1)
+ if (ielecont(j,1).eq.0) then
+ call readi(controlcard,'SCCONT',isccont(j,1),1)
+ endif
+ ang_cut(j)=ang_cut(j)*deg2rad
+ ang_cut1(j)=ang_cut1(j)*deg2rad
+ do k=1,npiece(j,1)
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'IFRAG1',ifrag(1,k,j),0)
+ call readi(controlcard,'IFRAG2',ifrag(2,k,j),0)
+ enddo
+ write(iout,*)"j",j," npiece",npiece(j,1)," ifrag",
+ & (ifrag(1,k,j),ifrag(2,k,j),
+ & k=1,npiece(j,1))," ang_cut",ang_cut(j)*rad2deg,
+ & " ang_cut1",ang_cut1(j)*rad2deg
+ write(iout,*)"n_shift",n_shift(1,j,1),n_shift(2,j,1)
+ write(iout,*)"nc_frac",nc_fragm(j,1)," nc_req",nc_req_setf(j,1)
+ write(iout,*)"irms",irms(j,1)," ielecont",ielecont(j,1),
+ & " ilocal",iloc(j)," isccont",isccont(j,1)
+ enddo
+c Read data pertaning to higher levels
+ do i=2,nlevel
+ call card_concat(controlcard,.true.)
+ call readi(controlcard,'NFRAG',NFRAG(i),0)
+ write (iout,*) "i",i," nfrag",nfrag(i)
+ do j=1,nfrag(i)
+ call card_concat(controlcard,.true.)
+ if (i.eq.2) then
+ call readi(controlcard,'ELCONT',ielecont(j,i),0)
+ if (ielecont(j,i).eq.0) then
+ call readi(controlcard,'SCCONT',isccont(j,i),1)
+ endif
+ call readi(controlcard,'RMS',irms(j,i),0)
+ else
+ ielecont(j,i)=0
+ isccont(j,i)=0
+ irms(j,i)=1
+ endif
+ call readi(controlcard,'NPIECE',npiece(j,i),0)
+ call readi(controlcard,'N_SHIFT1',n_shift(1,j,i),0)
+ call readi(controlcard,'N_SHIFT2',n_shift(2,j,i),0)
+ call multreadi(controlcard,'IPIECE',ipiece(1,j,i),
+ & npiece(j,i),0)
+ call reada(controlcard,'NC_FRAC',nc_fragm(j,i),0.5d0)
+ call readi(controlcard,'NC_REQ',nc_req_setf(j,i),0)
+ write(iout,*) "j",j," npiece",npiece(j,i)," n_shift",
+ & n_shift(1,j,i),n_shift(2,j,i)," ielecont",ielecont(j,i),
+ & " isccont",isccont(j,i)," irms",irms(j,i)
+ write(iout,*) "ipiece",(ipiece(k,j,i),k=1,npiece(j,i))
+ write(iout,*)"n_shift",n_shift(1,j,i),n_shift(2,j,i)
+ write(iout,*)"nc_frac",nc_fragm(j,i),
+ & " nc_req",nc_req_setf(j,i)
+ enddo
+ enddo
+ if (binary) write (iout,*) "Classes written in binary format."
+ return
+ 121 continue
+ call reada(controlcard,'ANGCUT_HEL',angcut_hel,50.0d0)
+ call reada(controlcard,'MAXANG_HEL',angcut1_hel,60.0d0)
+ call reada(controlcard,'ANGCUT_BET',angcut_bet,90.0d0)
+ call reada(controlcard,'MAXANG_BET',angcut1_bet,360.0d0)
+ call reada(controlcard,'ANGCUT_STRAND',angcut_strand,90.0d0)
+ call reada(controlcard,'MAXANG_STRAND',angcut1_strand,60.0d0)
+ call reada(controlcard,'FRAC_MIN',frac_min_set,0.666666d0)
+ call reada(controlcard,'NC_FRAC_HEL',ncfrac_hel,0.5d0)
+ call readi(controlcard,'NC_REQ_HEL',ncreq_hel,0)
+ call reada(controlcard,'NC_FRAC_BET',ncfrac_bet,0.5d0)
+ call reada(controlcard,'NC_FRAC_PAIR',ncfrac_pair,0.3d0)
+ call readi(controlcard,'NC_REQ_BET',ncreq_bet,0)
+ call readi(controlcard,'NC_REQ_PAIR',ncreq_pair,0)
+ call readi(controlcard,'NSHIFT_HEL',nshift_hel,3)
+ call readi(controlcard,'NSHIFT_BET',nshift_bet,3)
+ call readi(controlcard,'NSHIFT_STRAND',nshift_strand,3)
+ call readi(controlcard,'NSHIFT_PAIR',nshift_pair,3)
+ call readi(controlcard,'RMS_SINGLE',irms_single,0)
+ call readi(controlcard,'CONT_SINGLE',icont_single,1)
+ call readi(controlcard,'LOCAL_SINGLE',iloc_single,1)
+ call readi(controlcard,'RMS_PAIR',irms_pair,0)
+ call readi(controlcard,'CONT_PAIR',icont_pair,1)
+ call readi(controlcard,'SPLIT_BET',isplit_bet,0)
+ angcut_hel=angcut_hel*deg2rad
+ angcut1_hel=angcut1_hel*deg2rad
+ angcut_bet=angcut_bet*deg2rad
+ angcut1_bet=angcut1_bet*deg2rad
+ angcut_strand=angcut_strand*deg2rad
+ angcut1_strand=angcut1_strand*deg2rad
+ write (iout,*) "Automatic detection of structural elements"
+ write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,
+ & ' NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,
+ & ' RMS_SINGLE',irms_single,' CONT_SINGLE',icont_single,
+ & ' NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,
+ & ' RMS_PAIR',irms_pair,' CONT_PAIR',icont_pair,
+ & ' SPLIT_BET',isplit_bet
+ write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,
+ & ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
+ write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,
+ & ' MAXANG_HEL',angcut1_hel*rad2deg
+ write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,
+ & ' MAXANG_BET',angcut1_bet*rad2deg
+ write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,
+ & ' MAXANG_STRAND',angcut1_strand*rad2deg
+ write (iout,*) 'FRAC_MIN',frac_min_set
+ return
+ end
--- /dev/null
+ integer function rescode(iseq,nam,itype)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ character*3 nam,ucase
+
+ if (itype.eq.0) then
+
+ do i=1,ntyp1
+ if (ucase(nam).eq.restyp(i)) then
+ rescode=i
+ return
+ endif
+ enddo
+
+ else
+
+ do i=1,ntyp1
+ if (nam(1:1).eq.onelet(i)) then
+ rescode=i
+ return
+ endif
+ enddo
+
+ endif
+
+ write (iout,10) iseq,nam
+ stop
+ 10 format ('**** Error - residue',i4,' has an unresolved name ',a3)
+ end
+
--- /dev/null
+ double precision function rmscalc(ishif,i,j,jcon,lprn)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ double precision przes(3),obrot(3,3)
+ double precision creff(3,maxres2),cc(3,maxres2)
+ logical iadded(maxres)
+ integer inumber(2,maxres)
+ common /ccc/ creff,cc,iadded,inumber
+ logical lprn
+ logical non_conv
+ integer ishif,i,j
+ if (lprn) then
+ write (iout,*) "i",i," j",j," jcont",jcon," ishif",ishif
+ write (iout,*) "npiece",npiece(j,i)
+ endif
+ ii=0
+ do l=1,nres
+ iadded(l)=.false.
+ enddo
+ do k=1,npiece(j,i)
+ if (i.eq.1) then
+ if (lprn)
+ & write (iout,*) "Level 1: j=",j,"k=",k," adding fragment",
+ & ifrag(1,k,j),ifrag(2,k,j)
+ call cprep(ifrag(1,k,j),ifrag(2,k,j),ishif,ii)
+c write (iout,*) "ii=",ii
+ else
+ kk = ipiece(k,j,i)
+c write (iout,*) "kk",kk," npiece",npiece(kk,1)
+ do l=1,npiece(kk,1)
+ if (lprn)
+ & write (iout,*) "Level",i,": j=",j,"k=",k," kk=",kk,
+ & " l=",l," adding fragment",
+ & ifrag(1,l,kk),ifrag(2,l,kk)
+ call cprep(ifrag(1,l,kk),ifrag(2,l,kk),ishif,ii)
+ enddo
+ endif
+ enddo
+ if (lprn) then
+ do k=1,ii
+ write(iout,'(5i4,2(3f10.5,5x))') i,j,k,inumber(1,k),
+ & inumber(2,k),(creff(l,k),l=1,3),(cc(l,k),l=1,3)
+ enddo
+ endif
+ call fitsq(rms,cc(1,1),creff(1,1),ii,przes,obrot,non_conv)
+ if (non_conv) then
+ print *,'Error: FITSQ non-convergent, jcon',jcon
+ rmscalc=1.0d2
+ else if (rms.lt.-1.0d-6) then
+ print *,'Error: rms^2 = ',rms,jcon
+ rmscalc = 1.0d2
+ else if (rms.ge.1.0d-6 .and. rms.lt.0) then
+ rmscalc=0.0d0
+ else
+ rmscalc = dsqrt(rms)
+ endif
+ return
+ end
+c-------------------------------------------------------------------------
+ subroutine cprep(if1,if2,ishif,ii)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ double precision przes(3),obrot(3,3)
+ double precision creff(3,maxres2),cc(3,maxres2)
+ logical iadded(maxres)
+ integer inumber(2,maxres)
+ common /ccc/ creff,cc,iadded,inumber
+c write (iout,*) "Calling cprep"
+ do l=if1,if2
+c write (iout,*) "l",l," iadded",iadded(l)
+ if (l+ishif.gt.1 .and. l+ishif.le.nres .and. .not.iadded(l))
+ & then
+ ii=ii+1
+ iadded(l)=.true.
+ inumber(1,ii)=l
+ inumber(2,ii)=l+ishif
+ do m=1,3
+ creff(m,ii)=cref(m,l)
+ cc(m,ii)=c(m,l+ishif)
+ enddo
+ endif
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------
+ double precision function rmsnat(jcon)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ double precision przes(3),obrot(3,3)
+ logical non_conv
+ integer ishif,i,j
+ call fitsq(rms,c(1,nstart_sup),cref(1,nstart_sup),nsup,
+ & przes,obrot,non_conv)
+ if (non_conv) then
+ print *,'Error: FITSQ non-convergent, jcon',jcon
+ rmsnat=1.0d2
+ else if (rms.lt.-1.0d-6) then
+ print *,'Error: rms^2 = ',rms,jcon
+ rmsnat = 1.0d2
+ else if (rms.ge.1.0d-6 .and. rms.lt.0) then
+ rmsnat=0.0d0
+ else
+ rmsnat = dsqrt(rms)
+ endif
+ return
+ end
+c-----------------------------------------------------------------------------
+ double precision function gyrate(jcon)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CHAIN'
+ double precision cen(3),rg
+
+ do j=1,3
+ cen(j)=0.0d0
+ enddo
+
+ do i=nnt,nct
+ do j=1,3
+ cen(j)=cen(j)+c(j,i)
+ enddo
+ enddo
+ do j=1,3
+ cen(j)=cen(j)/dble(nct-nnt+1)
+ enddo
+ rg = 0.0d0
+ do i = nnt, nct
+ do j=1,3
+ rg = rg + (c(j,i)-cen(j))**2
+ enddo
+ end do
+ gyrate = dsqrt(rg/dble(nct-nnt+1))
+ return
+ end
--- /dev/null
+ subroutine define_fragments
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ include 'COMMON.FRAG'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CONTROL'
+ include 'COMMON.COMPAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.HEADER'
+ include 'COMMON.GEO'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.PEPTCONT'
+ include 'COMMON.INTERACT'
+ include 'COMMON.NAMES'
+ integer nstrand,istrand(2,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ character*16 strstr(4) /'helix','hairpin','strand','strand pair'/
+ write (iout,*) 'NC_FRAC_HEL',ncfrac_hel,' NC_REQ_HEL',ncreq_hel,
+ & 'NC_FRAC_BET',ncfrac_bet,' NC_REQ_BET',ncreq_bet,
+ & 'NC_FRAC_PAIR',ncfrac_pair,' NC_REQ_PAIR',ncreq_pair,
+ & ' RMS_PAIR',irms_pair,' SPLIT_BET',isplit_bet
+ write (iout,*) 'NSHIFT_HEL',nshift_hel,' NSHIFT_BET',nshift_bet,
+ & ' NSHIFT_STRAND',nshift_strand,' NSHIFT_PAIR',nshift_pair
+ write (iout,*) 'ANGCUT_HEL',angcut_hel*rad2deg,
+ & ' MAXANG_HEL',angcut1_hel*rad2deg
+ write (iout,*) 'ANGCUT_BET',angcut_bet*rad2deg,
+ & ' MAXANG_BET',angcut1_bet*rad2deg
+ write (iout,*) 'ANGCUT_STRAND',angcut_strand*rad2deg,
+ & ' MAXANG_STRAND',angcut1_strand*rad2deg
+ write (iout,*) 'FRAC_MIN',frac_min_set
+c Find secondary structure elements (helices and beta-sheets)
+ call secondary2(.true.,.false.,ncont_pept_ref,icont_pept_ref,
+ & isec_ref)
+c Define primary fragments. First include the helices.
+ nhairp=0
+ nstrand=0
+c Merge helices
+c AL 12/23/03 - to avoid splitting helices into very small fragments
+ if (merge_helices) then
+ write (iout,*) "Before merging helices: nhfrag",nhfrag
+ do i=1,nhfrag
+ write (2,*) hfrag(1,i),hfrag(2,i)
+ enddo
+ i=1
+ do while (i.lt.nhfrag)
+ if (hfrag(1,i+1)-hfrag(2,i).le.1) then
+ nhfrag=nhfrag-1
+ hfrag(2,i)=hfrag(2,i+1)
+ do j=i+1,nhfrag
+ hfrag(1,j)=hfrag(1,j+1)
+ hfrag(2,j)=hfrag(2,j+1)
+ enddo
+ endif
+ i=i+1
+ enddo
+ write (iout,*) "After merging helices: nhfrag",nhfrag
+ do i=1,nhfrag
+ write (2,*) hfrag(1,i),hfrag(2,i)
+ enddo
+ endif
+ nfrag(1)=nhfrag
+ do i=1,nhfrag
+ npiece(i,1)=1
+ ifrag(1,1,i)=hfrag(1,i)
+ ifrag(2,1,i)=hfrag(2,i)
+ n_shift(1,i,1)=0
+ n_shift(2,i,1)=nshift_hel
+ ang_cut(i)=angcut_hel
+ ang_cut1(i)=angcut1_hel
+ frac_min(i)=frac_min_set
+ nc_fragm(i,1)=ncfrac_hel
+ nc_req_setf(i,1)=ncreq_hel
+ istruct(i)=1
+ enddo
+ write (iout,*) "isplit_bet",isplit_bet
+ if (isplit_bet.gt.1) then
+c Split beta-sheets into strands and store strands as primary fragments.
+ call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+ do i=1,nstrand
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=istrand(1,i)
+ ifrag(2,1,ii)=istrand(2,i)
+ n_shift(1,ii,1)=nshift_strand
+ n_shift(2,ii,1)=nshift_strand
+ ang_cut(ii)=angcut_strand
+ ang_cut1(ii)=angcut1_strand
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=0
+ nc_req_setf(ii,1)=0
+ istruct(ii)=3
+ enddo
+ nfrag(1)=nfrag(1)+nstrand
+ else if (isplit_bet.eq.1) then
+c Split only far beta-sheets; does not split hairpins.
+ call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+ call split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+ do i=1,nhairp
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=ihairp(1,i)
+ ifrag(2,1,ii)=ihairp(2,i)
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=2
+ enddo
+ nfrag(1)=nfrag(1)+nhairp
+ do i=1,nstrand
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=istrand(1,i)
+ ifrag(2,1,ii)=istrand(2,i)
+ n_shift(1,ii,1)=nshift_strand
+ n_shift(2,ii,1)=nshift_strand
+ ang_cut(ii)=angcut_strand
+ ang_cut1(ii)=angcut1_strand
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=0
+ nc_req_setf(ii,1)=0
+ istruct(ii)=3
+ enddo
+ nfrag(1)=nfrag(1)+nstrand
+ else
+c Do not split beta-sheets; each pair of strands is a primary element.
+ call find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+ do i=1,nhairp
+ ii=i+nfrag(1)
+ npiece(ii,1)=1
+ ifrag(1,1,ii)=ihairp(1,i)
+ ifrag(2,1,ii)=ihairp(2,i)
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=2
+ enddo
+ nfrag(1)=nfrag(1)+nhairp
+ do i=1,nbfrag
+ ii=i+nfrag(1)
+ npiece(ii,1)=2
+ ifrag(1,1,ii)=bfrag(1,i)
+ ifrag(2,1,ii)=bfrag(2,i)
+ if (bfrag(3,i).lt.bfrag(4,i)) then
+ ifrag(1,2,ii)=bfrag(3,i)
+ ifrag(2,2,ii)=bfrag(4,i)
+ else
+ ifrag(1,2,ii)=bfrag(4,i)
+ ifrag(2,2,ii)=bfrag(3,i)
+ endif
+ n_shift(1,ii,1)=nshift_bet
+ n_shift(2,ii,1)=nshift_bet
+ ang_cut(ii)=angcut_bet
+ ang_cut1(ii)=angcut1_bet
+ frac_min(ii)=frac_min_set
+ nc_fragm(ii,1)=ncfrac_bet
+ nc_req_setf(ii,1)=ncreq_bet
+ istruct(ii)=4
+ enddo
+ nfrag(1)=nfrag(1)+nbfrag
+ endif
+ write (iout,*) "The following primary fragments were found:"
+ write (iout,*) "Helices:",nhfrag
+ do i=1,nhfrag
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ write (iout,*) "Hairpins:",nhairp
+ do i=nhfrag+1,nhfrag+nhairp
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,2x)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ write (iout,*) "Far strand pairs:",nbfrag
+ do i=nhfrag+nhairp+1,nhfrag+nhairp+nbfrag
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ i3=ifrag(1,2,i)
+ i4=ifrag(2,2,i)
+ it3=itype(i3)
+ it4=itype(i4)
+ write (iout,'(i3,2x,a,i4,2x,a,i4," and ",a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2,
+ & restyp(it3),i3,restyp(it4),i4
+ enddo
+ write (iout,*) "Strands:",nstrand
+ do i=nhfrag+nhairp+nbfrag+1,nfrag(1)
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ enddo
+ call imysort(nfrag(1),2,maxpiece,ifrag(1,1,1),npiece(1,1),
+ & istruct(1),n_shift(1,1,1),ang_cut(1),ang_cut1(1),frac_min(1),
+ & nc_fragm(1,1),nc_req_setf(1,1))
+ write (iout,*) "Fragments after sorting:"
+ do i=1,nfrag(1)
+ i1=ifrag(1,1,i)
+ i2=ifrag(2,1,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(i3,2x,a,i4,2x,a,i4,$)')
+ & i,restyp(it1),i1,restyp(it2),i2
+ if (npiece(i,1).eq.1) then
+ write (iout,'(2x,a)') strstr(istruct(i))
+ else
+ i1=ifrag(1,2,i)
+ i2=ifrag(2,2,i)
+ it1=itype(i1)
+ it2=itype(i2)
+ write (iout,'(2x,a,i4,2x,a,i4,2x,a)')
+ & restyp(it1),i1,restyp(it2),i2,strstr(istruct(i))
+ endif
+ enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine find_and_remove_hairpins(nbfrag,bfrag,nhairp,ihairp)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ integer nbfrag,bfrag(4,maxres/3)
+ integer nhairp,ihairp(2,maxres/5)
+ write (iout,*) "Entered find_and_remove_hairpins"
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ nhairp=0
+ i=1
+ do while (i.le.nbfrag)
+ write (iout,*) "check hairpin:",i,(bfrag(j,i),j=1,4)
+ if (bfrag(3,i).gt.bfrag(4,i) .and. bfrag(4,i)-bfrag(2,i).lt.5)
+ & then
+ write (iout,*) "Found hairpin:",i,bfrag(1,i),bfrag(3,i)
+ nhairp=nhairp+1
+ ihairp(1,nhairp)=bfrag(1,i)
+ ihairp(2,nhairp)=bfrag(3,i)
+ nbfrag=nbfrag-1
+ do j=i,nbfrag
+ do k=1,4
+ bfrag(k,j)=bfrag(k,j+1)
+ enddo
+ enddo
+ else
+ i=i+1
+ endif
+ enddo
+ write (iout,*) "After finding hairpins:"
+ write (iout,*) "nhairp",nhairp
+ do i=1,nhairp
+ write (iout,*) i,ihairp(1,i),ihairp(2,i)
+ enddo
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine split_beta(nbfrag,bfrag,nstrand,istrand,nhairp,ihairp)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ integer nbfrag,bfrag(4,maxres/3)
+ integer nstrand,istrand(2,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ logical found
+ write (iout,*) "Entered split_beta"
+ write (iout,*) "nbfrag",nbfrag
+ do i=1,nbfrag
+ write (iout,*) i,(bfrag(k,i),k=1,4)
+ enddo
+ nstrand=0
+ do i=1,nbfrag
+ write (iout,*) "calling add_strand:",i,bfrag(1,i),bfrag(2,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,
+ & bfrag(1,i),bfrag(2,i),found)
+ if (bfrag(3,i).lt.bfrag(4,i)) then
+ write (iout,*) "calling add_strand:",i,bfrag(3,i),bfrag(4,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,
+ & bfrag(3,i),bfrag(4,i),found)
+ else
+ write (iout,*) "calling add_strand:",i,bfrag(4,i),bfrag(3,i)
+ call add_strand(nstrand,istrand,nhairp,ihairp,
+ & bfrag(4,i),bfrag(3,i),found)
+ endif
+ enddo
+ nbfrag=0
+ write (iout,*) "Strands found:",nstrand
+ do i=1,nstrand
+ write (iout,*) i,istrand(1,i),istrand(2,i)
+ enddo
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine add_strand(nstrand,istrand,nhairp,ihairp,is1,is2,found)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.COMPAR'
+ include 'COMMON.IOUNITS'
+ integer nstrand,istrand(2,maxres/2)
+ integer nhairp,ihairp(2,maxres/5)
+ logical found
+ found=.false.
+ do j=1,nhairp
+ idelt=(ihairp(2,j)-ihairp(1,j))/6
+ if (is1.lt.ihairp(2,j)-idelt.and.is2.gt.ihairp(1,j)+idelt) then
+ write (iout,*) "strand",is1,is2," is part of hairpin",
+ & ihairp(1,j),ihairp(2,j)
+ return
+ endif
+ enddo
+ do j=1,nstrand
+ idelt=(istrand(2,j)-istrand(1,j))/3
+ if (is1.lt.istrand(2,j)-idelt.and.is2.gt.istrand(1,j)+idelt)
+ & then
+c The strand already exists in the array; update its ends if necessary.
+ write (iout,*) "strand",is1,is2," found at position",j,
+ & ":",istrand(1,j),istrand(2,j)
+ istrand(1,j)=min0(istrand(1,j),is1)
+ istrand(2,j)=max0(istrand(2,j),is2)
+ return
+ endif
+ enddo
+c The strand has not been found; add it to the array.
+ write (iout,*) "strand",is1,is2," added to the array."
+ found=.true.
+ nstrand=nstrand+1
+ istrand(1,nstrand)=is1
+ istrand(2,nstrand)=is2
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine secondary2(lprint,lprint_sec,ncont,icont,isecstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FRAG'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ integer ncont,icont(2,maxcont),isec(maxres,4),nsec(maxres),
+ & isecstr(maxres)
+ logical lprint,lprint_sec,not_done,freeres
+ double precision p1,p2
+ external freeres
+ character*1 csec(0:2) /'-','E','H'/
+ if (lprint) then
+ write (iout,*) "entered secondary2",ncont
+ write (iout,*) "nstart_sup",nstart_sup," nend_sup",nend_sup
+ do i=1,ncont
+ write (iout,*) icont(1,i),icont(2,i)
+ enddo
+ endif
+ do i=1,nres
+ isecstr(i)=0
+ enddo
+ nbfrag=0
+ nhfrag=0
+ do i=1,nres
+ isec(i,1)=0
+ isec(i,2)=0
+ nsec(i)=0
+ enddo
+
+c finding parallel beta
+cd write (iout,*) '------- looking for parallel beta -----------'
+ nbeta=0
+ nstrand=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if (i1.ge.nstart_sup .and. i1.le.nend_sup
+ & .and. j1.gt.nstart_sup .and. j1.le.nend_sup) then
+cd write (iout,*) "parallel",i1,j1
+ if(j1-i1.gt.5 .and. freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+cd write (iout,*) i1,j1
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j) .and.
+ & freeres(i1,j1,nsec,isec)) goto 5
+ enddo
+ not_done=.false.
+ 5 continue
+cd write (iout,*) i1,j1,not_done
+ enddo
+ j1=j1-1
+ i1=i1-1
+ if (i1-ii1.gt.1) then
+ ii1=max0(ii1-1,1)
+ jj1=max0(jj1-1,1)
+ nbeta=nbeta+1
+ if(lprint)write(iout,'(a,i3,4i4)')'parallel beta',
+ & nbeta,ii1,i1,jj1,j1
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1+1
+ bfrag(2,nbfrag)=i1+1
+ bfrag(3,nbfrag)=jj1+1
+ bfrag(4,nbfrag)=min0(j1+1,nres)
+
+ do ij=ii1,i1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+ do ij=jj1,j1
+ nsec(ij)=nsec(ij)+1
+ isec(ij,nsec(ij))=nbeta
+ enddo
+
+ if(lprint_sec) then
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-1,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-1,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nbeta.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",jj1-1,"..",j1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",jj1-1,"..",j1-1,"'"
+ endif
+ write(12,'(a8,4i4)')
+ & "SetNeigh",ii1-1,i1-1,jj1-1,j1-1
+ endif
+ endif
+ endif
+ endif ! i1.ge.nstart_sup .and. i1.le.nend_sup .and. i2.gt.nstart_sup .and. i2.le.nend_sup
+ enddo
+
+c finding antiparallel beta
+cd write (iout,*) '--------- looking for antiparallel beta ---------'
+
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ if (freeres(i1,j1,nsec,isec)) then
+ ii1=i1
+ jj1=j1
+cd write (iout,*) i1,j1
+
+ not_done=.true.
+ do while (not_done)
+ i1=i1+1
+ j1=j1-1
+ do j=1,ncont
+ if (i1.eq.icont(1,j).and.j1.eq.icont(2,j) .and.
+ & freeres(i1,j1,nsec,isec)) goto 6
+ enddo
+ not_done=.false.
+ 6 continue
+cd write (iout,*) i1,j1,not_done
+ enddo
+ i1=i1-1
+ j1=j1+1
+ if (i1-ii1.gt.1) then
+
+ nbfrag=nbfrag+1
+ bfrag(1,nbfrag)=ii1
+ bfrag(2,nbfrag)=min0(i1+1,nres)
+ bfrag(3,nbfrag)=min0(jj1+1,nres)
+ bfrag(4,nbfrag)=j1
+
+ nbeta=nbeta+1
+ iii1=max0(ii1-1,1)
+ do ij=iii1,i1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+ jjj1=max0(j1-1,1)
+ do ij=jjj1,jj1
+ nsec(ij)=nsec(ij)+1
+ if (nsec(ij).le.2) then
+ isec(ij,nsec(ij))=nbeta
+ endif
+ enddo
+
+
+ if (lprint_sec) then
+ write (iout,'(a,i3,4i4)')'antiparallel beta',
+ & nbeta,ii1-1,i1,jj1,j1-1
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-2,"..",i1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",ii1-2,"..",i1-1,"'"
+ endif
+ nstrand=nstrand+1
+ if (nstrand.le.9) then
+ write(12,'(a18,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",j1-2,"..",jj1-1,"'"
+ else
+ write(12,'(a18,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'strand",nstrand,
+ & "' 'num = ",j1-2,"..",jj1-1,"'"
+ endif
+ write(12,'(a8,4i4)')
+ & "SetNeigh",ii1-2,i1-1,jj1-1,j1-2
+ endif
+ endif
+ endif
+ enddo
+
+cd write (iout,*) "After beta:",nbfrag
+cd do i=1,nbfrag
+cd write (iout,*) (bfrag(j,i),j=1,4)
+cd enddo
+
+ if (nstrand.gt.0.and.lprint_sec) then
+ write(12,'(a27,$)') "DefPropRes 'sheet' 'strand1"
+ do i=2,nstrand
+ if (i.le.9) then
+ write(12,'(a9,i1,$)') " | strand",i
+ else
+ write(12,'(a9,i2,$)') " | strand",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+
+c finding alpha or 310 helix
+
+ nhelix=0
+ do i=1,ncont
+ i1=icont(1,i)
+ j1=icont(2,i)
+ p1=phi(i1+2)*rad2deg
+ p2=0.0
+ if (j1+2.le.nres) p2=phi(j1+2)*rad2deg
+
+
+ if (j1.eq.i1+3 .and.
+ & ((p1.ge.10.and.p1.le.80).or.i1.le.2).and.
+ & ((p2.ge.10.and.p2.le.80).or.j1.le.2.or.j1.ge.nres-3) )then
+cd if (j1.eq.i1+3) write (iout,*) "found 1-4 ",i1,j1,p1,p2
+co if (j1.eq.i1+4) write (iout,*) "found 1-5 ",i1,j1,p1,p2
+ ii1=i1
+ jj1=j1
+ if (nsec(ii1).eq.0) then
+ not_done=.true.
+ else
+ not_done=.false.
+ endif
+ do while (not_done)
+ i1=i1+1
+ j1=j1+1
+ do j=1,ncont
+ if (i1.eq.icont(1,j) .and. j1.eq.icont(2,j)) goto 10
+ enddo
+ not_done=.false.
+ 10 continue
+ p1=phi(i1+2)*rad2deg
+ p2=phi(j1+2)*rad2deg
+ if (p1.lt.10.or.p1.gt.80.or.p2.lt.10.or.p2.gt.80)
+ & not_done=.false.
+
+cd write (iout,*) i1,j1,not_done,p1,p2
+ enddo
+ j1=j1+1
+ if (j1-ii1.gt.4) then
+ nhelix=nhelix+1
+cd write (iout,*)'helix',nhelix,ii1,j1
+
+ nhfrag=nhfrag+1
+ hfrag(1,nhfrag)=ii1
+ hfrag(2,nhfrag)=j1
+
+ do ij=ii1,j1
+ nsec(ij)=-1
+ enddo
+ if (lprint_sec) then
+ write (iout,'(a,i3,2i4)') "Helix",nhelix,ii1-1,j1-1
+ if (nhelix.le.9) then
+ write(12,'(a17,i1,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'helix",nhelix,
+ & "' 'num = ",ii1-1,"..",j1-2,"'"
+ else
+ write(12,'(a17,i2,a9,i3,a2,i3,a1)')
+ & "DefPropRes 'helix",nhelix,
+ & "' 'num = ",ii1-1,"..",j1-2,"'"
+ endif
+ endif
+ endif
+ endif
+ enddo
+
+ if (nhelix.gt.0.and.lprint_sec) then
+ write(12,'(a26,$)') "DefPropRes 'helix' 'helix1"
+ do i=2,nhelix
+ if (nhelix.le.9) then
+ write(12,'(a8,i1,$)') " | helix",i
+ else
+ write(12,'(a8,i2,$)') " | helix",i
+ endif
+ enddo
+ write(12,'(a1)') "'"
+ endif
+
+ if (lprint_sec) then
+ write(12,'(a37)') "DefPropRes 'coil' '! (helix | sheet)'"
+ write(12,'(a20)') "XMacStand ribbon.mac"
+ endif
+
+ if (lprint) then
+
+ write(iout,*) 'UNRES seq:'
+ do j=1,nbfrag
+ write(iout,*) 'beta ',(bfrag(i,j),i=1,4)
+ enddo
+
+ do j=1,nhfrag
+ write(iout,*) 'helix ',(hfrag(i,j),i=1,2)
+ enddo
+
+ endif
+
+ do j=1,nbfrag
+ do k=min0(bfrag(1,j),bfrag(2,j)),max0(bfrag(1,j),bfrag(2,j))
+ isecstr(k)=1
+ enddo
+ do k=min0(bfrag(3,j),bfrag(4,j)),max0(bfrag(3,j),bfrag(4,j))
+ isecstr(k)=1
+ enddo
+ enddo
+ do j=1,nhfrag
+ do k=hfrag(1,j),hfrag(2,j)
+ isecstr(k)=2
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) "Secondary structure"
+ do i=1,nres,80
+ ist=i
+ ien=min0(i+79,nres)
+ write (iout,*)
+ write (iout,'(8(7x,i3))') (k,k=ist+9,ien,10)
+ write (iout,'(80a1)') (onelet(itype(k)),k=ist,ien)
+ write (iout,'(80a1)') (csec(isecstr(k)),k=ist,ien)
+ enddo
+ write (iout,*)
+ endif
+ return
+ end
+c-------------------------------------------------
+ logical function freeres(i,j,nsec,isec)
+ include 'DIMENSIONS'
+ integer isec(maxres,4),nsec(maxres)
+ freeres=.false.
+
+ if (nsec(i).gt.1.or.nsec(j).gt.1) return
+ do k=1,nsec(i)
+ do l=1,nsec(j)
+ if (isec(i,k).eq.isec(j,l)) return
+ enddo
+ enddo
+ freeres=.true.
+ return
+ end
+
--- /dev/null
+ subroutine setup_var
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+C Set up variable list.
+ ntheta=nres-2
+ nphi=nres-3
+ nvar=ntheta+nphi
+ nside=0
+ do i=2,nres-1
+ if (itype(i).ne.10) then
+ nside=nside+1
+ ialph(i,1)=nvar+nside
+ ialph(nside,2)=i
+ endif
+ enddo
+ if (indphi.gt.0) then
+ nvar=nphi
+ else if (indback.gt.0) then
+ nvar=nphi+ntheta
+ else
+ nvar=nvar+2*nside
+ endif
+cd write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
+ return
+ end
--- /dev/null
+ subroutine set_slices(is,ie,ts,te,iR,ib,iparm)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.PROTFILES'
+ include 'COMMON.OBCINKA'
+ include 'COMMON.PROT'
+ integer islice,iR,ib,iparm
+ integer is(MaxSlice),ie(MaxSlice),nrec_slice
+ double precision ts(MaxSlice),te(MaxSlice),time_slice
+
+ do islice=1,nslice
+ if (time_end_collect(iR,ib,iparm).ge.1.0d10) then
+ ts(islice)=time_start_collect(iR,ib,iparm)
+ te(islice)=time_end_collect(iR,ib,iparm)
+ nrec_slice=(rec_end(iR,ib,iparm)-
+ & rec_start(iR,ib,iparm)+1)/nslice
+ is(islice)=rec_start(iR,ib,iparm)+(islice-1)*nrec_slice
+ ie(islice)=rec_start(iR,ib,iparm)+islice*nrec_slice-1
+ else
+ time_slice=(time_end_collect(iR,ib,iparm)
+ & -time_start_collect(iR,ib,iparm))/nslice
+ ts(islice)=time_start_collect(iR,ib,iparm)+(islice-1)*
+ & time_slice
+ te(islice)=time_start_collect(iR,ib,iparm)+islice*time_slice
+ is(islice)=rec_start(iR,ib,iparm)
+ ie(islice)=rec_end(iR,ib,iparm)
+ endif
+ enddo
+
+ write (iout,*) "nrec_slice",nrec_slice," time_slice",time_slice
+ write (iout,*) "is",(is(islice),islice=1,nslice)
+ write (iout,*) "ie",(ie(islice),islice=1,nslice)
+ write (iout,*) "rec_start",
+ & rec_start(iR,ib,iparm)," rec_end",rec_end(iR,ib,iparm)
+ write (iout,*) "ts",(ts(islice),islice=1,nslice)
+ write (iout,*) "te",(te(islice),islice=1,nslice)
+ write (iout,*) "time_start",
+ & time_start_collect(iR,ib,iparm)," time_end",
+ & time_end_collect(iR,ib,iparm)
+ call flush(iout)
+
+ return
+ end
+c-----------------------------------------------------------------------------
+ integer function slice(irecord,time,is,ie,ts,te)
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.PROTFILES'
+ include 'COMMON.OBCINKA'
+ include 'COMMON.PROT'
+ integer is(MaxSlice),ie(MaxSlice),nrec_slice
+ double precision ts(MaxSlice),te(MaxSlice),time_slice
+ integer i,ii,irecord
+ double precision time
+
+c write (iout,*) "within slice nslice",nslice
+c call flush(iout)
+ if (irecord.lt.is(1) .or. time.lt.ts(1)) then
+ ii=0
+ else
+ ii=1
+ do while (ii.le.nslice .and.
+ & (irecord.lt.is(ii) .or. irecord.gt.ie(ii) .or.
+ & time.lt.ts(ii) .or. time.gt.te(ii)) )
+c write (iout,*) "ii",ii,time,ts(ii)
+c call flush(iout)
+ ii=ii+1
+ enddo
+ endif
+c write (iout,*) "end: ii",ii
+c call flush(iout)
+ slice=ii
+ return
+ end
--- /dev/null
+ subroutine store_parm(iparm)
+C
+C Store parameters of set IPARM
+C valence angles and the side chains and energy parameters.
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.SCROT'
+ include 'COMMON.SCCOR'
+ include 'COMMON.ALLPARM'
+ integer i,j,k,l,m,mm,iparm
+
+c Store weights
+ ww_all(1,iparm)=wsc
+ ww_all(2,iparm)=wscp
+ ww_all(3,iparm)=welec
+ ww_all(4,iparm)=wcorr
+ ww_all(5,iparm)=wcorr5
+ ww_all(6,iparm)=wcorr6
+ ww_all(7,iparm)=wel_loc
+ ww_all(8,iparm)=wturn3
+ ww_all(9,iparm)=wturn4
+ ww_all(10,iparm)=wturn6
+ ww_all(11,iparm)=wang
+ ww_all(12,iparm)=wscloc
+ ww_all(13,iparm)=wtor
+ ww_all(14,iparm)=wtor_d
+ ww_all(15,iparm)=wstrain
+ ww_all(16,iparm)=wvdwpp
+ ww_all(17,iparm)=wbond
+ ww_all(19,iparm)=wsccor
+c Store bond parameters
+ vbldp0_all(iparm)=vbldp0
+ akp_all(iparm)=akp
+ do i=1,ntyp
+ nbondterm_all(i,iparm)=nbondterm(i)
+ do j=1,nbondterm(i)
+ vbldsc0_all(j,i,iparm)=vbldsc0(j,i)
+ aksc_all(j,i,iparm)=aksc(j,i)
+ abond0_all(j,i,iparm)=abond0(j,i)
+ enddo
+ enddo
+c Store bond angle parameters
+#ifdef CRYST_THETA
+ do i=1,ntyp
+ a0thet_all(i,iparm)=a0thet(i)
+ do j=1,2
+ athet_all(j,i,iparm)=athet(j,i)
+ bthet_all(j,i,iparm)=bthet(j,i)
+ enddo
+ do j=0,3
+ polthet_all(j,i,iparm)=polthet(j,i)
+ enddo
+ do j=1,3
+ gthet_all(j,i,iparm)=gthet(j,i)
+ enddo
+ theta0_all(i,iparm)=theta0(i)
+ sig0_all(i,iparm)=sig0(i)
+ sigc0_all(i,iparm)=sigc0(i)
+ enddo
+#else
+ nthetyp_all(iparm)=nthetyp
+ ntheterm_all(iparm)=ntheterm
+ ntheterm2_all(iparm)=ntheterm2
+ ntheterm3_all(iparm)=ntheterm3
+ nsingle_all(iparm)=nsingle
+ ndouble_all(iparm)=ndouble
+ nntheterm_all(iparm)=nntheterm
+ do i=1,ntyp1
+ ithetyp_all(i,iparm)=ithetyp(i)
+ enddo
+ do i=1,maxthetyp1
+ do j=1,maxthetyp1
+ do k=1,maxthetyp1
+ aa0thet_all(i,j,k,iparm)=aa0thet(i,j,k)
+ do l=1,ntheterm
+ aathet_all(l,i,j,k,iparm)=aathet(l,i,j,k)
+ enddo
+ do l=1,ntheterm2
+ do m=1,nsingle
+ bbthet_all(m,l,i,j,k,iparm)=bbthet(m,l,i,j,k)
+ ccthet_all(m,l,i,j,k,iparm)=ccthet(m,l,i,j,k)
+ ddthet_all(m,l,i,j,k,iparm)=ddthet(m,l,i,j,k)
+ eethet_all(m,l,i,j,k,iparm)=eethet(m,l,i,j,k)
+ enddo
+ enddo
+ do l=1,ntheterm3
+ do m=1,ndouble
+ do mm=1,ndouble
+ ffthet_all(mm,m,l,i,j,k,iparm)=ffthet(mm,m,l,i,j,k)
+ ggthet_all(mm,m,l,i,j,k,iparm)=ggthet(mm,m,l,i,j,k)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+#endif
+#ifdef CRYST_SC
+c Store the sidechain rotamer parameters
+ do i=1,ntyp
+ nlob_all(i,iparm)=nlob(i)
+ do j=1,nlob(i)
+ bsc_all(j,i,iparm)=bsc(j,i)
+ do k=1,3
+ censc_all(k,j,i,iparm)=censc(k,j,i)
+ enddo
+ do k=1,3
+ do l=1,3
+ gaussc_all(l,k,j,i,iparm)=gaussc(l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+#else
+ do i=1,ntyp
+ do j=1,65
+ sc_parmin_all(j,i,iparm)=sc_parmin(j,i)
+ enddo
+ enddo
+#endif
+c Store the torsional parameters
+ do i=1,ntortyp
+ do j=1,ntortyp
+ v0_all(i,j,iparm)=v0(i,j)
+ nterm_all(i,j,iparm)=nterm(i,j)
+ nlor_all(i,j,iparm)=nlor(i,j)
+ do k=1,nterm(i,j)
+ v1_all(k,i,j,iparm)=v1(k,i,j)
+ v2_all(k,i,j,iparm)=v2(i,i,j)
+ enddo
+ do k=1,nlor(i,j)
+ vlor1_all(k,i,j,iparm)=vlor1(k,i,j)
+ vlor2_all(k,i,j,iparm)=vlor2(k,i,j)
+ vlor3_all(k,i,j,iparm)=vlor3(k,i,j)
+ enddo
+ enddo
+ enddo
+c Store the double torsional parameters
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
+ ntermd1_all(i,j,k,iparm)=ntermd_1(i,j,k)
+ ntermd2_all(i,j,k,iparm)=ntermd_2(i,j,k)
+ do l=1,ntermd_1(i,j,k)
+ v1c_all(1,l,i,j,k,iparm)=v1c(1,l,i,j,k)
+ v1c_all(2,l,i,j,k,iparm)=v1c(2,l,i,j,k)
+ v2c_all(1,l,i,j,k,iparm)=v2c(1,l,i,j,k)
+ v2c_all(2,l,i,j,k,iparm)=v2c(2,l,i,j,k)
+ enddo
+ do l=1,ntermd_2(i,j,k)
+ do m=1,ntermd_2(i,j,k)
+ v2s_all(l,m,i,j,k,iparm)=v2s(l,m,i,j,k)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+c Store parameters of the cumulants
+ do i=1,nloctyp
+ do j=1,2
+ b1_all(j,i,iparm)=b1(j,i)
+ b1tilde_all(j,i,iparm)=b1tilde(j,i)
+ b2_all(j,i,iparm)=b2(j,i)
+ enddo
+ do j=1,2
+ do k=1,2
+ cc_all(k,j,i,iparm)=cc(k,j,i)
+ ctilde_all(k,j,i,iparm)=ctilde(k,j,i)
+ dd_all(k,j,i,iparm)=dd(k,j,i)
+ dtilde_all(k,j,i,iparm)=dtilde(k,j,i)
+ ee_all(k,j,i,iparm)=ee(k,j,i)
+ enddo
+ enddo
+ enddo
+c Store the parameters of electrostatic interactions
+ do i=1,2
+ do j=1,2
+ app_all(j,i,iparm)=app(j,i)
+ bpp_all(j,i,iparm)=bpp(j,i)
+ ael6_all(j,i,iparm)=ael6(j,i)
+ ael3_all(j,i,iparm)=ael3(j,i)
+ enddo
+ enddo
+c Store sidechain parameters
+ do i=1,ntyp
+ do j=1,ntyp
+ aa_all(j,i,iparm)=aa(j,i)
+ bb_all(j,i,iparm)=bb(j,i)
+ r0_all(j,i,iparm)=r0(j,i)
+ sigma_all(j,i,iparm)=sigma(j,i)
+ chi_all(j,i,iparm)=chi(j,i)
+ chipp_all(j,i,iparm)=chipp(j,i)
+ augm_all(j,i,iparm)=augm(j,i)
+ eps_all(j,i,iparm)=eps(j,i)
+ sigmap1_all(j,i,iparm)=sigmap1(j,i)
+ sigmap2_all(j,i,iparm)=sigmap2(j,i)
+ chis_all(j,i,iparm)=chis(j,i)
+ do k=1,4
+ alphasur_all(k,j,i,iparm)=alphasur(k,j,i)
+ wstate_all(k,j,i,iparm)=wstate(k,j,i)
+ enddo
+ nstate_all(j,i,iparm)=nstate(j,i)
+ do k=1,2
+ do l=1,2
+ dhead_all(l,k,j,i,iparm)=dhead(l,k,j,i)
+ enddo
+ enddo
+ do k=1,2
+ dtail_all(k,j,i,iparm)=dtail(k,j,i)
+ enddo
+ epshead_all(j,i,iparm)=epshead(j,i)
+ rborn_all(j,i,iparm)=rborn(j,i)
+ do k=1,2
+ wqdip_all(k,j,i,iparm)=wqdip(k,j,i)
+ enddo
+ wquad_all(j,i,iparm)=wquad(j,i)
+ alphapol_all(j,i,iparm)=alphapol(j,i)
+ do k=1,4
+ alphiso_all(k,j,i,iparm)=alphiso(k,j,i)
+ enddo
+ sigiso1_all(j,i,iparm)=sigiso1(j,i)
+ sigiso2_all(j,i,iparm)=sigiso2(j,i)
+ epsintab_all(j,i,iparm)=epsintab(j,i)
+ enddo
+ enddo
+ do i=1,ntyp
+ chip_all(i,iparm)=chip(i)
+ alp_all(i,iparm)=alp(i)
+ enddo
+c Store the SCp parameters
+ do i=1,ntyp
+ do j=1,2
+ aad_all(i,j,iparm)=aad(i,j)
+ bad_all(i,j,iparm)=bad(i,j)
+ enddo
+ enddo
+c Store disulfide-bond parameters
+ ebr_all(iparm)=ebr
+ d0cm_all(iparm)=d0cm
+ akcm_all(iparm)=akcm
+ akth_all(iparm)=akth
+ akct_all(iparm)=akct
+ v1ss_all(iparm)=v1ss
+ v2ss_all(iparm)=v2ss
+ v3ss_all(iparm)=v3ss
+c Store SC-backbone correlation parameters
+ do i=1,nsccortyp
+ do j=1,nsccortyp
+
+ nterm_sccor_all(j,i,iparm)=nterm_sccor(j,i)
+ do l=1,3
+ do k=1,nterm_sccor(j,i)
+ v1sccor_all(k,l,j,i,iparm)=v1sccor(k,l,j,i)
+ v2sccor_all(k,l,j,i,iparm)=v2sccor(k,l,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine restore_parm(iparm)
+C
+C Store parameters of set IPARM
+C valence angles and the side chains and energy parameters.
+C
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ include 'DIMENSIONS.FREE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.FFIELD'
+ include 'COMMON.NAMES'
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.SCROT'
+ include 'COMMON.SCCOR'
+ include 'COMMON.ALLPARM'
+ integer i,j,k,l,m,mm,iparm
+
+c Restore weights
+ wsc=ww_all(1,iparm)
+ wscp=ww_all(2,iparm)
+ welec=ww_all(3,iparm)
+ wcorr=ww_all(4,iparm)
+ wcorr5=ww_all(5,iparm)
+ wcorr6=ww_all(6,iparm)
+ wel_loc=ww_all(7,iparm)
+ wturn3=ww_all(8,iparm)
+ wturn4=ww_all(9,iparm)
+ wturn6=ww_all(10,iparm)
+ wang=ww_all(11,iparm)
+ wscloc=ww_all(12,iparm)
+ wtor=ww_all(13,iparm)
+ wtor_d=ww_all(14,iparm)
+ wstrain=ww_all(15,iparm)
+ wvdwpp=ww_all(16,iparm)
+ wbond=ww_all(17,iparm)
+ wsccor=ww_all(19,iparm)
+c Restore bond parameters
+ vbldp0=vbldp0_all(iparm)
+ akp=akp_all(iparm)
+ do i=1,ntyp
+ nbondterm(i)=nbondterm_all(i,iparm)
+ do j=1,nbondterm(i)
+ vbldsc0(j,i)=vbldsc0_all(j,i,iparm)
+ aksc(j,i)=aksc_all(j,i,iparm)
+ abond0(j,i)=abond0_all(j,i,iparm)
+ enddo
+ enddo
+c Restore bond angle parameters
+#ifdef CRYST_THETA
+ do i=1,ntyp
+ a0thet(i)=a0thet_all(i,iparm)
+ do j=1,2
+ athet(j,i)=athet_all(j,i,iparm)
+ bthet(j,i)=bthet_all(j,i,iparm)
+ enddo
+ do j=0,3
+ polthet(j,i)=polthet_all(j,i,iparm)
+ enddo
+ do j=1,3
+ gthet(j,i)=gthet_all(j,i,iparm)
+ enddo
+ theta0(i)=theta0_all(i,iparm)
+ sig0(i)=sig0_all(i,iparm)
+ sigc0(i)=sigc0_all(i,iparm)
+ enddo
+#else
+ nthetyp=nthetyp_all(iparm)
+ ntheterm=ntheterm_all(iparm)
+ ntheterm2=ntheterm2_all(iparm)
+ ntheterm3=ntheterm3_all(iparm)
+ nsingle=nsingle_all(iparm)
+ ndouble=ndouble_all(iparm)
+ nntheterm=nntheterm_all(iparm)
+ do i=1,ntyp1
+ ithetyp(i)=ithetyp_all(i,iparm)
+ enddo
+ do i=1,maxthetyp1
+ do j=1,maxthetyp1
+ do k=1,maxthetyp1
+ aa0thet(i,j,k)=aa0thet_all(i,j,k,iparm)
+ do l=1,ntheterm
+ aathet(l,i,j,k)=aathet_all(l,i,j,k,iparm)
+ enddo
+ do l=1,ntheterm2
+ do m=1,nsingle
+ bbthet(m,l,i,j,k)=bbthet_all(m,l,i,j,k,iparm)
+ ccthet(m,l,i,j,k)=ccthet_all(m,l,i,j,k,iparm)
+ ddthet(m,l,i,j,k)=ddthet_all(m,l,i,j,k,iparm)
+ eethet(m,l,i,j,k)=eethet_all(m,l,i,j,k,iparm)
+ enddo
+ enddo
+ do l=1,ntheterm3
+ do m=1,ndouble
+ do mm=1,ndouble
+ ffthet(mm,m,l,i,j,k)=ffthet_all(mm,m,l,i,j,k,iparm)
+ ggthet(mm,m,l,i,j,k)=ggthet_all(mm,m,l,i,j,k,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+#endif
+c Restore the sidechain rotamer parameters
+#ifdef CRYST_SC
+ do i=1,ntyp
+ nlob(i)=nlob_all(i,iparm)
+ do j=1,nlob(i)
+ bsc(j,i)=bsc_all(j,i,iparm)
+ do k=1,3
+ censc(k,j,i)=censc_all(k,j,i,iparm)
+ enddo
+ do k=1,3
+ do l=1,3
+ gaussc(l,k,j,i)=gaussc_all(l,k,j,i,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
+#else
+ do i=1,ntyp
+ do j=1,65
+ sc_parmin(j,i)=sc_parmin_all(j,i,iparm)
+ enddo
+ enddo
+#endif
+c Restore the torsional parameters
+ do i=1,ntortyp
+ do j=1,ntortyp
+ v0(i,j)=v0_all(i,j,iparm)
+ nterm(i,j)=nterm_all(i,j,iparm)
+ nlor(i,j)=nlor_all(i,j,iparm)
+ do k=1,nterm(i,j)
+ v1(k,i,j)=v1_all(k,i,j,iparm)
+ v2(i,i,j)=v2_all(k,i,j,iparm)
+ enddo
+ do k=1,nlor(i,j)
+ vlor1(k,i,j)=vlor1_all(k,i,j,iparm)
+ vlor2(k,i,j)=vlor2_all(k,i,j,iparm)
+ vlor3(k,i,j)=vlor3_all(k,i,j,iparm)
+ enddo
+ enddo
+ enddo
+c Restore the double torsional parameters
+ do i=1,ntortyp
+ do j=1,ntortyp
+ do k=1,ntortyp
+ ntermd_1(i,j,k)=ntermd1_all(i,j,k,iparm)
+ ntermd_2(i,j,k)=ntermd2_all(i,j,k,iparm)
+ do l=1,ntermd_1(i,j,k)
+ v1c(1,l,i,j,k)=v1c_all(1,l,i,j,k,iparm)
+ v1c(2,l,i,j,k)=v1c_all(2,l,i,j,k,iparm)
+ v2c(1,l,i,j,k)=v2c_all(1,l,i,j,k,iparm)
+ v2c(2,l,i,j,k)=v2c_all(2,l,i,j,k,iparm)
+ enddo
+ do l=1,ntermd_2(i,j,k)
+ do m=1,ntermd_2(i,j,k)
+ v2s(l,m,i,j,k)=v2s_all(l,m,i,j,k,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+c Restore parameters of the cumulants
+ do i=1,nloctyp
+ do j=1,2
+ b1(j,i)=b1_all(j,i,iparm)
+ b1tilde(j,i)=b1tilde_all(j,i,iparm)
+ b2(j,i)=b2_all(j,i,iparm)
+ enddo
+ do j=1,2
+ do k=1,2
+ cc(k,j,i)=cc_all(k,j,i,iparm)
+ ctilde(k,j,i)=ctilde_all(k,j,i,iparm)
+ dd(k,j,i)=dd_all(k,j,i,iparm)
+ dtilde(k,j,i)=dtilde_all(k,j,i,iparm)
+ ee(k,j,i)=ee_all(k,j,i,iparm)
+ enddo
+ enddo
+ enddo
+c Restore the parameters of electrostatic interactions
+ do i=1,2
+ do j=1,2
+ app(j,i)=app_all(j,i,iparm)
+ bpp(j,i)=bpp_all(j,i,iparm)
+ ael6(j,i)=ael6_all(j,i,iparm)
+ ael3(j,i)=ael3_all(j,i,iparm)
+ enddo
+ enddo
+c Restore sidechain parameters
+ do i=1,ntyp
+ do j=1,ntyp
+ aa(j,i)=aa_all(j,i,iparm)
+ bb(j,i)=bb_all(j,i,iparm)
+ r0(j,i)=r0_all(j,i,iparm)
+ sigma(j,i)=sigma_all(j,i,iparm)
+ chi(j,i)=chi_all(j,i,iparm)
+ chipp(j,i)=chipp_all(j,i,iparm)
+ augm(j,i)=augm_all(j,i,iparm)
+ eps(j,i)=eps_all(j,i,iparm)
+ sigmap1(j,i)=sigmap1_all(j,i,iparm)
+ sigmap2(j,i)=sigmap2_all(j,i,iparm)
+ chis(j,i)=chis_all(j,i,iparm)
+ do k=1,4
+ alphasur(k,j,i)=alphasur_all(k,j,i,iparm)
+ wstate(k,j,i)=wstate_all(k,j,i,iparm)
+ enddo
+ nstate(j,i)=nstate_all(j,i,iparm)
+ do k=1,2
+ do l=1,2
+ dhead(l,k,j,i)=dhead_all(l,k,j,i,iparm)
+ enddo
+ enddo
+ do k=1,2
+ dtail(k,j,i)=dtail_all(k,j,i,iparm)
+ enddo
+ epshead(j,i)=epshead_all(j,i,iparm)
+ rborn(j,i)=rborn_all(j,i,iparm)
+ do k=1,2
+ wqdip(k,j,i)=wqdip_all(k,j,i,iparm)
+ enddo
+ wquad(j,i)=wquad_all(j,i,iparm)
+ alphapol(j,i)=alphapol_all(j,i,iparm)
+ do k=1,4
+ alphiso(k,j,i)=alphiso_all(k,j,i,iparm)
+ enddo
+ sigiso1(j,i)=sigiso1_all(j,i,iparm)
+ sigiso2(j,i)=sigiso2_all(j,i,iparm)
+ epsintab(j,i)=epsintab_all(j,i,iparm)
+ enddo
+ enddo
+ do i=1,ntyp
+ chip(i)=chip_all(i,iparm)
+ alp(i)=alp_all(i,iparm)
+ enddo
+c Restore the SCp parameters
+ do i=1,ntyp
+ do j=1,2
+ aad(i,j)=aad_all(i,j,iparm)
+ bad(i,j)=bad_all(i,j,iparm)
+ enddo
+ enddo
+c Restore disulfide-bond parameters
+ ebr=ebr_all(iparm)
+ d0cm=d0cm_all(iparm)
+ akcm=akcm_all(iparm)
+ akth=akth_all(iparm)
+ akct=akct_all(iparm)
+ v1ss=v1ss_all(iparm)
+ v2ss=v2ss_all(iparm)
+ v3ss=v3ss_all(iparm)
+c Restore SC-backbone correlation parameters
+ do i=1,nsccortyp
+ do j=1,nsccortyp
+
+ nterm_sccor(j,i)=nterm_sccor_all(j,i,iparm)
+c do i=1,20
+c do j=1,20
+ do l=1,3
+ do k=1,nterm_sccor(j,i)
+ v1sccor(k,l,j,i)=v1sccor_all(k,l,j,i,iparm)
+ v2sccor(k,l,j,i)=v2sccor_all(k,l,j,i,iparm)
+ enddo
+ enddo
+ enddo
+ enddo
+ return
+ end
--- /dev/null
+C $Date: 1994/10/05 16:41:52 $
+C $Revision: 2.2 $
+C
+C
+C
+ subroutine set_timers
+c
+ implicit none
+ double precision tcpu
+ include 'COMMON.TIME1'
+C Diminish the assigned time limit a little so that there is some time to
+C end a batch job
+c timlim=batime-150.0
+C Calculate the initial time, if it is not zero (e.g. for the SUN).
+ stime=tcpu()
+cd print *,' in SET_TIMERS stime=',stime
+ return
+ end
+C------------------------------------------------------------------------------
+ logical function stopx(nf)
+C This function returns .true. in case of time up on the master node.
+ implicit none
+ include 'DIMENSIONS'
+ include 'DIMENSIONS.ZSCOPT'
+ integer nf
+ logical ovrtim
+#ifdef MPI
+ include 'mpif.h'
+ include 'COMMON.MPI'
+#endif
+ include 'COMMON.IOUNITS'
+ include 'COMMON.TIME1'
+ if (ovrtim()) then
+C Finish if time is up.
+ stopx = .true.
+ WhatsUp=1
+ else if (cutoffviol) then
+ stopx = .true.
+ WhatsUp=2
+ else
+ stopx=.false.
+ endif
+ return
+ end
+C--------------------------------------------------------------------------
+ logical function ovrtim()
+ implicit none
+ include 'COMMON.TIME1'
+ real*8 tcpu,curtim
+ curtim= tcpu()
+c print *,'curtim=',curtim,' timlim=',timlim
+C curtim is the current time in seconds.
+c ovrtim=(curtim .ge. timlim - safety )
+c ovrtim does not work sometimes and crashes the program ! CHUUUJ !
+c setting always to false
+ ovrtim=.false.
+ return
+ end
+**************************************************************************
+ double precision function tcpu()
+ implicit none
+ include 'COMMON.TIME1'
+#ifdef ES9000
+****************************
+C Next definition for EAGLE (ibm-es9000)
+ real*8 micseconds
+ integer rcode
+ tcpu=cputime(micseconds,rcode)
+ tcpu=(micseconds/1.0E6) - stime
+****************************
+#endif
+#ifdef SUN
+****************************
+C Next definitions for sun
+ REAL*8 ECPU,ETIME,ETCPU
+ dimension tarray(2)
+ tcpu=etime(tarray)
+ tcpu=tarray(1)
+****************************
+#endif
+#ifdef KSR
+****************************
+C Next definitions for ksr
+C this function uses the ksr timer ALL_SECONDS from the PMON library to
+C return the elapsed time in seconds
+ tcpu= all_seconds() - stime
+****************************
+#endif
+#ifdef SGI
+****************************
+C Next definitions for sgi
+ real timar(2), etime, seconds
+ seconds = etime(timar)
+Cd print *,'seconds=',seconds,' stime=',stime
+C usrsec = timar(1)
+C syssec = timar(2)
+ tcpu=seconds - stime
+****************************
+#endif
+
+#ifdef LINUX
+****************************
+C Next definitions for sgi
+ real timar(2), etime, seconds
+ seconds = etime(timar)
+Cd print *,'seconds=',seconds,' stime=',stime
+C usrsec = timar(1)
+C syssec = timar(2)
+ tcpu=seconds - stime
+****************************
+#endif
+
+
+#ifdef CRAY
+****************************
+C Next definitions for Cray
+C call date(curdat)
+C curdat=curdat(1:9)
+C call clock(curtim)
+C curtim=curtim(1:8)
+ cpusec = second()
+ tcpu=cpusec - stime
+****************************
+#endif
+#ifdef AIX
+****************************
+C Next definitions for RS6000
+ integer*4 i1,mclock
+ i1 = mclock()
+ tcpu = (i1+0.0D0)/100.0D0
+#endif
+#ifdef WIN
+****************************
+c next definitions for windows NT Digital fortran
+ real time_real
+ call cpu_time(time_real)
+ tcpu = time_real
+#endif
+
+ return
+ end
+C---------------------------------------------------------------------------
+ subroutine dajczas(rntime,hrtime,mintime,sectime)
+ implicit none
+ include 'COMMON.IOUNITS'
+ integer ihr,imn,isc
+ real*8 rntime,hrtime,mintime,sectime
+ hrtime=rntime/3600.0D0
+ hrtime=aint(hrtime)
+ mintime=aint((rntime-3600.0D0*hrtime)/60.0D0)
+ sectime=aint((rntime-3600.0D0*hrtime-60.0D0*mintime)+0.5D0)
+ if (sectime.eq.60.0D0) then
+ sectime=0.0D0
+ mintime=mintime+1.0D0
+ endif
+ ihr=hrtime
+ imn=mintime
+ isc=sectime
+ write (iout,328) ihr,imn,isc
+ 328 FORMAT(//'***** Computation time: ',I4 ,' hours ',I2 ,
+ 1 ' minutes ', I2 ,' seconds *****')
+ return
+ end
--- /dev/null
+ subroutine WHAM_CALC(islice,*)
+! Weighed Histogram Analysis Method (WHAM) code
+! Written by A. Liwo based on the work of Kumar et al.,
+! J.Comput.Chem., 13, 1011 (1992)
+!
+! 2/1/05 Multiple temperatures allowed.
+! 2/2/05 Free energies calculated directly from data points
+! acc. to Eq. (21) of Kumar et al.; final histograms also
+! constructed based on this equation.
+! 2/12/05 Multiple parameter sets included
+!
+! 2/2/05 Parallel version
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ integer MaxBinRms,MaxBinRgy
+ parameter (MaxBinRms=100,MaxBinRgy=100)
+ integer MaxHdim
+c parameter (MaxHdim=200000)
+ parameter (MaxHdim=100)
+ integer maxinde
+ parameter (maxinde=100)
+#ifdef MPI
+ include "mpif.h"
+ include "COMMON.MPI"
+ integer ierror,errcode,status(MPI_STATUS_SIZE)
+#endif
+ include "COMMON.CONTROL"
+ include "COMMON.IOUNITS"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.FFIELD"
+ include "COMMON.SBRIDGE"
+ include "COMMON.PROT"
+ include "COMMON.ENEPS"
+ integer MaxPoint,MaxPointProc
+ parameter (MaxPoint=MaxStr,
+ & MaxPointProc=MaxStr_Proc)
+ double precision finorm_max,potfac,entmin,entmax,expfac,vf
+ double precision entfac_min,entfac_min_t
+ parameter (finorm_max=1.0d0)
+ integer islice
+ integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln
+ integer start,end,iharm,ib,iib,nbin1,nbin,nbin_rms,nbin_rgy,
+ & nbin_rmsrgy,liczba,iparm,nFi,indrgy,indrms
+ integer htot(0:MaxHdim),histent(0:2000)
+ double precision v(MaxPointProc,MaxR,MaxT_h,Max_Parm)
+ double precision energia(0:max_ene)
+#ifdef MPI
+ integer tmax_t,upindE_p
+ double precision fi_p(MaxR,MaxT_h,Max_Parm),
+ & fi_p_min(MaxR,MaxT_h,Max_Parm)
+ double precision sumW_p(0:Max_GridT,Max_Parm),
+ & sumE_p(0:Max_GridT,Max_Parm),sumEsq_p(0:Max_GridT,Max_Parm),
+ & sumQ_p(MaxQ1,0:Max_GridT,Max_Parm),
+ & sumQsq_p(MaxQ1,0:Max_GridT,Max_Parm),
+ & sumEQ_p(MaxQ1,0:Max_GridT,Max_Parm),
+ & sumEprim_p(MaxQ1,0:Max_GridT,Max_Parm),
+ & sumEbis_p(0:Max_GridT,Max_Parm)
+ double precision hfin_p(0:MaxHdim,maxT_h),
+ & hfin_ent_p(0:MaxHdim),histE_p(0:maxindE),sumH,
+ & hrmsrgy_p(0:MaxBinRgy,0:MaxBinRms,maxT_h)
+ double precision rgymin_t,rmsmin_t,rgymax_t,rmsmax_t
+ double precision potEmin_t_all(maxT_h,Max_Parm),entmin_p,entmax_p
+ integer histent_p(0:2000)
+ logical lprint /.true./
+#endif
+ double precision rgymin,rmsmin,rgymax,rmsmax
+ double precision sumW(0:NGridT,Max_Parm),sumE(0:NGridT,Max_Parm),
+ & sumEsq(0:NGridT,Max_Parm),sumQ(MaxQ1,0:NGridT,Max_Parm),
+ & sumQsq(MaxQ1,0:NGridT,Max_Parm),sumEQ(MaxQ1,0:NGridT,Max_Parm),
+ & sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT,
+ & weight,econstr
+ double precision fi(MaxR,maxT_h,Max_Parm),
+ & fi_min(MaxR,maxT_h,Max_Parm),
+ & dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom,
+ & hfin(0:MaxHdim,maxT_h),histE(0:maxindE),
+ & hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h),
+ & potEmin_all(maxT_h,Max_Parm),potEmin,potEmin_min,ent,
+ & hfin_ent(0:MaxHdim),vmax,aux
+ double precision fT(6),fTprim(6),fTbis(6),quot,quotl1,quotl,kfacl,
+ & eprim,ebis,temper,kfac/2.4d0/,T0/300.0d0/,
+ & eplus,eminus,logfac,tanhT,tt
+ double precision etot,evdw,evdw_t,evdw2,ees,evdw1,ebe,etors,
+ & escloc,ehpb,ecorr,ecorr5,ecorr6,eello_turn4,eello_turn3,
+ & eturn6,eel_loc,edihcnstr,etors_d,estr,evdw2_14,esccor
+
+ integer ind_point(maxpoint),upindE,indE
+ character*16 plik
+ character*1 licz1
+ character*2 licz2
+ character*3 licz3
+ character*128 nazwa
+ integer ilen
+ external ilen
+
+ write (iout,*) "Enter WHAM_calc"
+ call flush(iout)
+ write(licz2,'(bz,i2.2)') islice
+ nbin1 = 1.0d0/delta
+ write (iout,'(//80(1h-)/"Solving WHAM equations for slice",
+ & i2/80(1h-)//)') islice
+ write (iout,*) "delta",delta," nbin1",nbin1
+ write (iout,*) "MaxN",MaxN," MaxQ",MaxQ," MaHdim",MaxHdim
+ call flush(iout)
+ dmin=0.0d0
+ tmax=0
+ do i=1,nParmset
+ do j=1,nT_h(i)
+ potEmin_all(j,i)=1.0d10
+ enddo
+ enddo
+ rgymin=1.0d10
+ rmsmin=1.0d10
+ rgymax=0.0d0
+ rmsmax=0.0d0
+ do t=0,MaxN
+ htot(t)=0
+ enddo
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+ if (q(nQ+1,i).lt.rmsmin) rmsmin=q(nQ+1,i)
+ if (q(nQ+1,i).gt.rmsmax) rmsmax=q(nQ+1,i)
+ if (q(nQ+2,i).lt.rgymin) rgymin=q(nQ+2,i)
+ if (q(nQ+2,i).gt.rgymax) rgymax=q(nQ+2,i)
+ ind_point(i)=0
+ do j=nQ,1,-1
+ ind=(q(j,i)-dmin+1.0d-8)/delta
+ if (j.eq.1) then
+ ind_point(i)=ind_point(i)+ind
+ else
+ ind_point(i)=ind_point(i)+nbin1**(j-1)*ind
+ endif
+ if (ind_point(i).lt.0 .or. ind_point(i).gt.MaxHdim) then
+ write (iout,*) "Error - index exceeds range for point",i,
+ & " q=",q(j,i)," ind",ind_point(i)
+#ifdef MPI
+ write (iout,*) "Processor",me1
+ call flush(iout)
+ call MPI_Abort(MPI_COMM_WORLD, Ierror, Errcode )
+#endif
+ stop
+ endif
+ enddo ! j
+ if (ind_point(i).gt.tmax) tmax=ind_point(i)
+ htot(ind_point(i))=htot(ind_point(i))+1
+#ifdef DEBUG
+ write (iout,*) "i",i,"q",(q(j,i),j=1,nQ)," ind",ind_point(i),
+ & " htot",htot(ind_point(i))
+ call flush(iout)
+#endif
+ enddo ! i
+ call flush(iout)
+
+ nbin=nbin1**nQ-1
+ write (iout,'(a)') "Numbers of counts in Q bins"
+ do t=0,tmax
+ if (htot(t).gt.0) then
+ write (iout,'(i15,$)') t
+ liczba=t
+ do j=1,nQ
+ jj = mod(liczba,nbin1)
+ liczba=liczba/nbin1
+ write (iout,'(i5,$)') jj
+ enddo
+ write (iout,'(i8)') htot(t)
+ endif
+ enddo
+ do iparm=1,nParmSet
+ write (iout,'(a,i3)') "Number of data points for parameter set",
+ & iparm
+ write (iout,'(i7,$)') ((snk(m,ib,iparm,islice),m=1,nr(ib,iparm)),
+ & ib=1,nT_h(iparm))
+ write (iout,'(i8)') stot(islice)
+ write (iout,'(a)')
+ enddo
+ call flush(iout)
+
+#ifdef MPI
+ call MPI_AllReduce(tmax,tmax_t,1,MPI_INTEGER,MPI_MAX,
+ & WHAM_COMM,IERROR)
+ tmax=tmax_t
+ call MPI_AllReduce(rmsmin,rmsmin_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MIN,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rmsmax,rmsmax_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MAX,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rgymin,rgymin_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MIN,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rgymax,rgymax_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MAX,WHAM_COMM,IERROR)
+ rgymin=rgymin_t
+ rgymax=rgymax_t
+ rmsmin=rmsmin_t
+ rmsmax=rmsmax_t
+#endif
+ rmsmin=deltrms*dint(rmsmin/deltrms)
+ rmsmax=deltrms*dint(rmsmax/deltrms)
+ rgymin=deltrms*dint(rgymin/deltrgy)
+ rgymax=deltrms*dint(rgymax/deltrgy)
+ nbin_rms=(rmsmax-rmsmin)/deltrms
+ nbin_rgy=(rgymax-rgymin)/deltrgy
+ write (iout,*) "rmsmin",rmsmin," rmsmax",rmsmax," rgymin",rgymin,
+ & " rgymax",rgymax," nbin_rms",nbin_rms," nbin_rgy",nbin_rgy
+ nFi=0
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ nFi=nFi+nR(j,i)
+ enddo
+ enddo
+ write (iout,*) "nFi",nFi
+! Compute the Boltzmann factor corresponing to restrain potentials in different
+! simulations.
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+c write (9,'(3i5,f10.5)') i,(iparm,potE(i,iparm),iparm=1,nParmSet)
+ do iparm=1,nParmSet
+#ifdef DEBUG
+ write (iout,'(2i5,21f8.2)') i,iparm,
+ & (enetb(k,i,iparm),k=1,21)
+#endif
+ call restore_parm(iparm)
+#ifdef DEBUG
+ write (iout,*) wsc,wscp,welec,wvdwpp,wang,wtor,wscloc,
+ & wcorr,wcorr5,wcorr6,wturn4,wturn3,wturn6,wel_loc,
+ & wtor_d,wsccor,wbond
+#endif
+ do ib=1,nT_h(iparm)
+ if (rescale_mode.eq.1) then
+ quot=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ fT(l)=kfacl/(kfacl-1.0d0+quotl)
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+ else if (rescale_mode.eq.2) then
+ quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+ quotl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ fT(l)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
+ else if (rescale_mode.eq.0) then
+ do l=1,6
+ fT(l)=1.0d0
+ enddo
+ else
+ write (iout,*) "Error in WHAM_CALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+ evdw=enetb(1,i,iparm)
+ evdw_t=enetb(21,i,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,i,iparm)
+ evdw2=enetb(2,i,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,i,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,i,iparm)
+ evdw1=enetb(16,i,iparm)
+#else
+ ees=enetb(3,i,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,i,iparm)
+ ecorr5=enetb(5,i,iparm)
+ ecorr6=enetb(6,i,iparm)
+ eel_loc=enetb(7,i,iparm)
+ eello_turn3=enetb(8,i,iparm)
+ eello_turn4=enetb(9,i,iparm)
+ eturn6=enetb(10,i,iparm)
+ ebe=enetb(11,i,iparm)
+ escloc=enetb(12,i,iparm)
+ etors=enetb(13,i,iparm)
+ etors_d=enetb(14,i,iparm)
+ ehpb=enetb(15,i,iparm)
+ estr=enetb(18,i,iparm)
+ esccor=enetb(19,i,iparm)
+ edihcnstr=enetb(20,i,iparm)
+#ifdef DEBUG
+ write (iout,'(3i5,6f5.2,14f12.3)') i,ib,iparm,(ft(l),l=1,6),
+ & evdw+evdw_t,evdw2,ees,evdw1,ecorr,eel_loc,estr,ebe,escloc,
+ & etors,etors_d,eello_turn3,eello_turn4,esccor
+#endif
+
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#endif
+#ifdef DEBUG
+ write (iout,*) i,iparm,1.0d0/(beta_h(ib,iparm)*1.987D-3),
+ & etot
+#endif
+#ifdef DEBUG
+ if (iparm.eq.1 .and. ib.eq.1) then
+ write (iout,*)"Conformation",i
+ energia(0)=etot
+ do k=1,max_ene
+ energia(k)=enetb(k,i,iparm)
+ enddo
+ call enerprint(energia(0),fT)
+ endif
+#endif
+ do kk=1,nR(ib,iparm)
+ Econstr=0.0d0
+ do j=1,nQ
+ dd = q(j,i)
+ Econstr=Econstr+Kh(j,kk,ib,iparm)
+ & *(dd-q0(j,kk,ib,iparm))**2
+ enddo
+ v(i,kk,ib,iparm)=
+ & -beta_h(ib,iparm)*(etot+Econstr)
+#ifdef DEBUG
+ write (iout,'(4i5,4e15.5)') i,kk,ib,iparm,
+ & etot,v(i,kk,ib,iparm)
+#endif
+ enddo ! kk
+ enddo ! ib
+ enddo ! iparm
+ enddo ! i
+! Simple iteration to calculate free energies corresponding to all simulation
+! runs.
+ do iter=1,maxit
+
+! Compute new free-energy values corresponding to the righ-hand side of the
+! equation and their derivatives.
+ write (iout,*) "------------------------fi"
+ entfac_min=1.0d10
+#ifdef MPI
+ do t=1,scount(me1)
+#else
+ do t=1,ntot(islice)
+#endif
+ vmax=-1.0d+20
+ do i=1,nParmSet
+ do k=1,nT_h(i)
+ do l=1,nR(k,i)
+ vf=v(t,l,k,i)+f(l,k,i)
+ if (vf.gt.vmax) vmax=vf
+ enddo
+ enddo
+ enddo
+ denom=0.0d0
+ do i=1,nParmSet
+ do k=1,nT_h(i)
+ do l=1,nR(k,i)
+ aux=f(l,k,i)+v(t,l,k,i)-vmax
+ if (aux.gt.-200.0d0)
+ & denom=denom+snk(l,k,i,islice)*dexp(aux)
+ enddo
+ enddo
+ enddo
+ entfac(t)=-dlog(denom)-vmax
+ if (entfac(t).lt.entfac_min) entfac_min=entfac(t)
+#ifdef DEBUG
+ write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t)
+#endif
+ enddo
+c#ifdef MPI
+c write (iout,*) "entfac_min before AllReduce",entfac_min
+c call MPI_AllReduce(entfac_min,entfac_min_t,1,
+c & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+c entfac_min=entfac_min_t
+c write (iout,*) "entfac_min after AllReduce",entfac_min
+c#endif
+c#ifdef MPI
+c do t=1,scount(me)
+c entfac(t)=entfac(t)-entfac_min
+c enddo
+c#else
+c do t=1,ntot(islice)
+c entfac(t)=entfac(t)-entfac_min
+c enddo
+c#endif
+ do iparm=1,nParmSet
+ do iib=1,nT_h(iparm)
+ do ii=1,nR(iib,iparm)
+#ifdef MPI
+ fi_p_min(ii,iib,iparm)=-1.0d10
+ do t=1,scount(me)
+ aux=v(t,ii,iib,iparm)+entfac(t)
+ if (aux.gt.fi_p_min(ii,iib,iparm))
+ & fi_p_min(ii,iib,iparm)=aux
+ enddo
+#else
+ do t=1,ntot(islice)
+ aux=v(t,ii,iib,iparm)+entfac(t)
+ if (aux.gt.fi_min(ii,iib,iparm))
+ & fi_min(ii,iib,iparm)=aux
+ enddo
+#endif
+ enddo ! ii
+ enddo ! iib
+ enddo ! iparm
+#ifdef MPI
+#ifdef DEBUG
+ write (iout,*) "fi_min before AllReduce"
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ write (iout,*) (i,j,k,fi_p_min(k,j,i),k=1,nR(j,i))
+ enddo
+ enddo
+#endif
+ call MPI_AllReduce(fi_p_min,fi_min,MaxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+#ifdef DEBUG
+ write (iout,*) "fi_min after AllReduce"
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ write (iout,*) (i,j,k,fi_min(k,j,i),k=1,nR(j,i))
+ enddo
+ enddo
+#endif
+#endif
+ do iparm=1,nParmSet
+ do iib=1,nT_h(iparm)
+ do ii=1,nR(iib,iparm)
+#ifdef MPI
+ fi_p(ii,iib,iparm)=0.0d0
+ do t=1,scount(me)
+ fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm)
+ & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))
+#ifdef DEBUG
+ write (iout,'(4i5,4e15.5)') t,ii,iib,iparm,
+ & v(t,ii,iib,iparm),entfac(t),fi_min(ii,iib,iparm),
+ & fi_p(ii,iib,iparm)
+#endif
+ enddo
+#else
+ fi(ii,iib,iparm)=0.0d0
+ do t=1,ntot(islice)
+ fi(ii,iib,iparm)=fi(ii,iib,iparm)
+ & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))
+ enddo
+#endif
+ enddo ! ii
+ enddo ! iib
+ enddo ! iparm
+
+#ifdef MPI
+#ifdef DEBUG
+ write (iout,*) "fi before MPI_Reduce me",me,' master',master
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ write (iout,*) "iparm",iparm," ib",ib
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ write (iout,'(8e15.5)') (fi_p(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+#endif
+#ifdef DEBUG
+ write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet,
+ & maxR*MaxT_h*nParmSet
+ write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
+ & " WHAM_COMM",WHAM_COMM
+#endif
+ call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,
+ & MPI_SUM,Master,WHAM_COMM,IERROR)
+#ifdef DEBUG
+ write (iout,*) "fi after MPI_Reduce nparmset",nparmset
+ do iparm=1,nParmSet
+ write (iout,*) "iparm",iparm
+ do ib=1,nT_h(iparm)
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ write (iout,'(8e15.5)') (fi(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+#endif
+ if (me1.eq.Master) then
+#endif
+ avefi=0.0d0
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))-fi_min(i,ib,iparm)
+ avefi=avefi+fi(i,ib,iparm)
+ enddo
+ enddo
+ enddo
+ avefi=avefi/nFi
+ do iparm=1,nParmSet
+ write (iout,*) "Parameter set",iparm
+ do ib =1,nT_h(iparm)
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ do i=1,nR(ib,iparm)
+ fi(i,ib,iparm)=fi(i,ib,iparm)-avefi
+ enddo
+ write (iout,'(8f10.5)') (fi(i,ib,iparm),i=1,nR(ib,iparm))
+ write (iout,'(8f10.5)') (f(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+
+! Compute the norm of free-energy increments.
+ finorm=0.0d0
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ finorm=finorm+dabs(fi(i,ib,iparm)-f(i,ib,iparm))
+ f(i,ib,iparm)=fi(i,ib,iparm)
+ enddo
+ enddo
+ enddo
+
+ write (iout,*) 'Iteration',iter,' finorm',finorm
+
+#ifdef MPI
+ endif
+ call MPI_Bcast(f(1,1,1),MaxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Bcast(finorm,1,MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM,IERROR)
+#endif
+! Exit, if the increment norm is smaller than pre-assigned tolerance.
+ if (finorm.lt.fimin) then
+ write (iout,*) 'Iteration converged'
+ goto 20
+ endif
+
+ enddo ! iter
+
+ 20 continue
+! Now, put together the histograms from all simulations, in order to get the
+! unbiased total histogram.
+
+C Determine the minimum free energies
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+c write (9,'(3i5,f10.5)') i,(iparm,potE(i,iparm),iparm=1,nParmSet)
+ do iparm=1,nParmSet
+#ifdef DEBUG
+ write (iout,'(2i5,21f8.2)') i,iparm,
+ & (enetb(k,i,iparm),k=1,21)
+#endif
+ call restore_parm(iparm)
+#ifdef DEBUG
+ write (iout,*) wsc,wscp,welec,wvdwpp,wang,wtor,wscloc,
+ & wcorr,wcorr5,wcorr6,wturn4,wturn3,wturn6,wel_loc,
+ & wtor_d,wsccor,wbond
+#endif
+ do ib=1,nT_h(iparm)
+ if (rescale_mode.eq.1) then
+ quot=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ fT(l)=kfacl/(kfacl-1.0d0+quotl)
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+ else if (rescale_mode.eq.2) then
+ quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+ quotl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ fT(l)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
+ else if (rescale_mode.eq.0) then
+ do l=1,6
+ fT(l)=1.0d0
+ enddo
+ else
+ write (iout,*) "Error in WHAM_CALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+ evdw=enetb(1,i,iparm)
+ evdw_t=enetb(21,i,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,i,iparm)
+ evdw2=enetb(2,i,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,i,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,i,iparm)
+ evdw1=enetb(16,i,iparm)
+#else
+ ees=enetb(3,i,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,i,iparm)
+ ecorr5=enetb(5,i,iparm)
+ ecorr6=enetb(6,i,iparm)
+ eel_loc=enetb(7,i,iparm)
+ eello_turn3=enetb(8,i,iparm)
+ eello_turn4=enetb(9,i,iparm)
+ eturn6=enetb(10,i,iparm)
+ ebe=enetb(11,i,iparm)
+ escloc=enetb(12,i,iparm)
+ etors=enetb(13,i,iparm)
+ etors_d=enetb(14,i,iparm)
+ ehpb=enetb(15,i,iparm)
+ estr=enetb(18,i,iparm)
+ esccor=enetb(19,i,iparm)
+ edihcnstr=enetb(20,i,iparm)
+#ifdef DEBUG
+ write (iout,'(3i5,6f5.2,14f12.3)') i,ib,iparm,(ft(l),l=1,6),
+ & evdw+evdw_t,evdw2,ees,evdw1,ecorr,eel_loc,estr,ebe,escloc,
+ & etors,etors_d,eello_turn3,eello_turn4,esccor,edihcnstr
+#endif
+
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#endif
+c write (iout,*) "i",i," ib",ib,
+c & " temp",1.0d0/(1.987d-3*beta_h(ib,iparm))," etot",etot,
+c & " entfac",entfac(i)
+ etot=etot-entfac(i)/beta_h(ib,iparm)
+ if(etot.lt.potEmin_all(ib,iparm)) potEmin_all(ib,iparm)=etot
+c write (iout,*) "efree",etot," potEmin",potEmin_all(ib,iparm)
+ enddo ! ib
+ enddo ! iparm
+ enddo ! i
+#ifdef DEBUG
+ write (iout,*) "The potEmin array before reduction"
+ do i=1,nParmSet
+ write (iout,*) "Parameter set",i
+ do j=1,nT_h(i)
+ write (iout,*) j,PotEmin_all(j,i)
+ enddo
+ enddo
+ write (iout,*) "potEmin_min",potEmin_min
+#endif
+#ifdef MPI
+C Determine the minimum energes for all parameter sets and temperatures
+ call MPI_AllReduce(potEmin_all(1,1),potEmin_t_all(1,1),
+ & maxT_h*nParmSet,MPI_DOUBLE_PRECISION,MPI_MIN,WHAM_COMM,IERROR)
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ potEmin_all(j,i)=potEmin_t_all(j,i)
+ enddo
+ enddo
+#endif
+ potEmin_min=potEmin_all(1,1)
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ if (potEmin_all(j,i).lt.potEmin_min)
+ & potEmin_min=potEmin_all(j,i)
+ enddo
+ enddo
+#ifdef DEBUG
+ write (iout,*) "The potEmin array"
+ do i=1,nParmSet
+ write (iout,*) "Parameter set",i
+ do j=1,nT_h(i)
+ write (iout,*) j,PotEmin_all(j,i)
+ enddo
+ enddo
+ write (iout,*) "potEmin_min",potEmin_min
+#endif
+
+#ifdef MPI
+ do t=0,tmax
+ hfin_ent_p(t)=0.0d0
+ enddo
+#else
+ do t=0,tmax
+ hfin_ent(t)=0.0d0
+ enddo
+#endif
+ write (iout,*) "--------------hist"
+#ifdef MPI
+ do iparm=1,nParmSet
+ do i=0,nGridT
+ sumW_p(i,iparm)=0.0d0
+ sumE_p(i,iparm)=0.0d0
+ sumEbis_p(i,iparm)=0.0d0
+ sumEsq_p(i,iparm)=0.0d0
+ do j=1,nQ+2
+ sumQ_p(j,i,iparm)=0.0d0
+ sumQsq_p(j,i,iparm)=0.0d0
+ sumEQ_p(j,i,iparm)=0.0d0
+ enddo
+ enddo
+ enddo
+ upindE_p=0
+#else
+ do iparm=1,nParmSet
+ do i=0,nGridT
+ sumW(i,iparm)=0.0d0
+ sumE(i,iparm)=0.0d0
+ sumEbis(i,iparm)=0.0d0
+ sumEsq(i,iparm)=0.0d0
+ do j=1,nQ+2
+ sumQ(j,i,iparm)=0.0d0
+ sumQsq(j,i,iparm)=0.0d0
+ sumEQ(j,i,iparm)=0.0d0
+ enddo
+ enddo
+ enddo
+ upindE=0
+#endif
+c 8/26/05 entropy distribution
+#ifdef MPI
+ entmin_p=1.0d10
+ entmax_p=-1.0d10
+ do t=1,scount(me1)
+c ent=-dlog(entfac(t))
+ ent=entfac(t)
+ if (ent.lt.entmin_p) entmin_p=ent
+ if (ent.gt.entmax_p) entmax_p=ent
+ enddo
+ write (iout,*) "entmin",entmin_p," entmax",entmax_p
+ call flush(iout)
+ call MPI_Allreduce(entmin_p,entmin,1,MPI_DOUBLE_PRECISION,MPI_MIN,
+ & WHAM_COMM,IERROR)
+ call MPI_Allreduce(entmax_p,entmax,1,MPI_DOUBLE_PRECISION,MPI_MAX,
+ & WHAM_COMM,IERROR)
+ ientmax=entmax-entmin
+ if (ientmax.gt.2000) ientmax=2000
+ write (iout,*) "entmin",entmin," entmax",entmax," ientmax",ientmax
+ call flush(iout)
+ do t=1,scount(me1)
+c ient=-dlog(entfac(t))-entmin
+ ient=entfac(t)-entmin
+ if (ient.le.2000) histent_p(ient)=histent_p(ient)+1
+ enddo
+ call MPI_Allreduce(histent_p(0),histent(0),ientmax+1,MPI_INTEGER,
+ & MPI_SUM,WHAM_COMM,IERROR)
+ if (me1.eq.Master) then
+ write (iout,*) "Entropy histogram"
+ do i=0,ientmax
+ write(iout,'(f15.4,i10)') entmin+i,histent(i)
+ enddo
+ endif
+#else
+ entmin=1.0d10
+ entmax=-1.0d10
+ do t=1,ntot(islice)
+ ent=entfac(t)
+ if (ent.lt.entmin) entmin=ent
+ if (ent.gt.entmax) entmax=ent
+ enddo
+ ientmax=-dlog(entmax)-entmin
+ if (ientmax.gt.2000) ientmax=2000
+ do t=1,ntot(islice)
+ ient=entfac(t)-entmin
+ if (ient.le.2000) histent(ient)=histent(ient)+1
+ enddo
+ write (iout,*) "Entropy histogram"
+ do i=0,ientmax
+ write(iout,'(2f15.4)') entmin+i,histent(i)
+ enddo
+#endif
+
+#ifdef MPI
+c write (iout,*) "me1",me1," scount",scount(me1)
+
+ do iparm=1,nParmSet
+
+#ifdef MPI
+ do ib=1,nT_h(iparm)
+ do t=0,tmax
+ hfin_p(t,ib)=0.0d0
+ enddo
+ enddo
+ do i=1,maxindE
+ histE_p(i)=0.0d0
+ enddo
+#else
+ do ib=1,nT_h(iparm)
+ do t=0,tmax
+ hfin(t,ib)=0.0d0
+ enddo
+ enddo
+ do i=1,maxindE
+ histE(i)=0.0d0
+ enddo
+#endif
+ do ib=1,nT_h(iparm)
+ do i=0,MaxBinRms
+ do j=0,MaxBinRgy
+ hrmsrgy(j,i,ib)=0.0d0
+#ifdef MPI
+ hrmsrgy_p(j,i,ib)=0.0d0
+#endif
+ enddo
+ enddo
+ enddo
+
+ do t=1,scount(me1)
+#else
+ do t=1,ntot(islice)
+#endif
+ ind = ind_point(t)
+#ifdef MPI
+ hfin_ent_p(ind)=hfin_ent_p(ind)+dexp(entfac(t))
+#else
+ hfin_ent(ind)=hfin_ent(ind)+dexp(entfac(t))
+#endif
+ call restore_parm(iparm)
+ evdw=enetb(21,t,iparm)
+ evdw_t=enetb(1,t,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,t,iparm)
+ evdw2=enetb(2,t,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,t,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,t,iparm)
+ evdw1=enetb(16,t,iparm)
+#else
+ ees=enetb(3,t,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,t,iparm)
+ ecorr5=enetb(5,t,iparm)
+ ecorr6=enetb(6,t,iparm)
+ eel_loc=enetb(7,t,iparm)
+ eello_turn3=enetb(8,t,iparm)
+ eello_turn4=enetb(9,t,iparm)
+ eturn6=enetb(10,t,iparm)
+ ebe=enetb(11,t,iparm)
+ escloc=enetb(12,t,iparm)
+ etors=enetb(13,t,iparm)
+ etors_d=enetb(14,t,iparm)
+ ehpb=enetb(15,t,iparm)
+ estr=enetb(18,t,iparm)
+ esccor=enetb(19,t,iparm)
+ edihcnstr=enetb(20,t,iparm)
+ do k=0,nGridT
+ betaT=startGridT+k*delta_T
+ temper=betaT
+c fT=T0/betaT
+c ft=2*T0/(T0+betaT)
+ if (rescale_mode.eq.1) then
+ quot=betaT/T0
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ denom=kfacl-1.0d0+quotl
+ fT(l)=kfacl/denom
+ ftprim(l)=-l*ft(l)*quotl1/(T0*denom)
+ ftbis(l)=l*kfacl*quotl1*
+ & (2*l*quotl-(l-1)*denom)/(quot*t0*t0*denom**3)
+ enddo
+#if defined(FUNCTH)
+ ft(6)=(320.0d0+80.0d0*dtanh((betaT-320.0d0)/80.0d0))/
+ & 320.0d0
+ ftprim(6)=1.0d0/(320.0d0*dcosh((betaT-320.0d0)/80.0d0)**2)
+ ftbis(6)=-2.0d0*dtanh((betaT-320.0d0)/80.0d0)
+ & /(320.0d0*80.0d0*dcosh((betaT-320.0d0)/80.0d0)**3)
+#elif defined(FUNCT)
+ fT(6)=betaT/T0
+ ftprim(6)=1.0d0/T0
+ ftbis(6)=0.0d0
+#else
+ fT(6)=1.0d0
+ ftprim(6)=0.0d0
+ ftbis(6)=0.0d0
+#endif
+ else if (rescale_mode.eq.2) then
+ quot=betaT/T0
+ quotl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ eplus=dexp(quotl)
+ eminus=dexp(-quotl)
+ logfac=1.0d0/dlog(eplus+eminus)
+ tanhT=(eplus-eminus)/(eplus+eminus)
+ fT(l)=1.12692801104297249644d0*logfac
+ ftprim(l)=-l*quotl1*ft(l)*tanhT*logfac/T0
+ ftbis(l)=(l-1)*ftprim(l)/(quot*T0)-
+ & 2*l*quotl1/T0*logfac*
+ & (2*l*quotl1*ft(l)/(T0*(eplus+eminus)**2)
+ & +ftprim(l)*tanhT)
+ enddo
+#if defined(FUNCTH)
+ ft(6)=(320.0d0+80.0d0*dtanh((betaT-320.0d0)/80.0d0))/
+ & 320.0d0
+ ftprim(6)=1.0d0/(320.0d0*dcosh((betaT-320.0d0)/80.0d0)**2)
+ ftbis(6)=-2.0d0*dtanh((betaT-320.0d0)/80.0d0)
+ & /(320.0d0*80.0d0*dcosh((betaT-320.0d0)/80.0d0)**3)
+#elif defined(FUNCT)
+ fT(6)=betaT/T0
+ ftprim(6)=1.0d0/T0
+ ftbis(6)=0.0d0
+#else
+ fT(6)=1.0d0
+ ftprim(6)=0.0d0
+ ftbis(6)=0.0d0
+#endif
+ else if (rescale_mode.eq.0) then
+ do l=1,5
+ fT(l)=1.0d0
+ ftprim(l)=0.0d0
+ enddo
+ else
+ write (iout,*) "Error in WHAM_CALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+c write (iout,*) "ftprim",ftprim
+c write (iout,*) "ftbis",ftbis
+ betaT=1.0d0/(1.987D-3*betaT)
+ if (betaT.ge.beta_h(1,iparm)) then
+ potEmin=potEmin_all(1,iparm)
+c write(iout,*) "first",temper,potEmin
+ else if (betaT.lt.beta_h(nT_h(iparm),iparm)) then
+ potEmin=potEmin_all(nT_h(iparm),iparm)
+c write (iout,*) "last",temper,potEmin
+ else
+ do l=1,nT_h(iparm)-1
+ if (betaT.le.beta_h(l,iparm) .and.
+ & betaT.gt.beta_h(l+1,iparm)) then
+ potEmin=potEmin_all(l,iparm)
+c write (iout,*) "l",l,
+c & betaT,1.0d0/(1.987D-3*beta_h(l,iparm)),
+c & 1.0d0/(1.987D-3*beta_h(l+1,iparm)),temper,potEmin
+ exit
+ endif
+ enddo
+ endif
+c write (iout,*) ib," PotEmin",potEmin
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+ eprim=ftprim(6)*evdw_t+ftprim(1)*welec*ees
+ & +ftprim(1)*wtor*etors+
+ & ftprim(3)*wcorr*ecorr+ftprim(4)*wcorr5*ecorr5+
+ & ftprim(5)*wcorr6*ecorr6+ftprim(3)*wturn4*eello_turn4+
+ & ftprim(2)*wturn3*eello_turn3+ftprim(5)*wturn6*eturn6+
+ & ftprim(2)*wel_loc*eel_loc+ftprim(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+ ebis=ftbis(1)*welec*ees+ftbis(1)*wtor*etors+
+ & ftbis(3)*wcorr*ecorr+ftbis(4)*wcorr5*ecorr5+
+ & ftbis(5)*wcorr6*ecorr6+ftbis(3)*wturn4*eello_turn4+
+ & ftbis(2)*wturn3*eello_turn3+ftbis(5)*wturn6*eturn6+
+ & ftbis(2)*wel_loc*eel_loc+ftbis(2)*wtor_d*etors_d+
+ & ftbis(1)*wsccor*esccor
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+ eprim=ftprim(6)*evdw_t+ftprim(1)*welec*(ees+evdw1)
+ & +ftprim(1)*wtor*etors+
+ & ftprim(3)*wcorr*ecorr+ftprim(4)*wcorr5*ecorr5+
+ & ftprim(5)*wcorr6*ecorr6+ftprim(3)*wturn4*eello_turn4+
+ & ftprim(2)*wturn3*eello_turn3+ftprim(5)*wturn6*eturn6+
+ & ftprim(2)*wel_loc*eel_loc+ftprim(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+ ebis=ftbis(1)*welec*(ees+evdw1)+ftbis(1)*wtor*etors+
+ & ftbis(3)*wcorr*ecorr+ftbis(4)*wcorr5*ecorr5+
+ & ftbis(5)*wcorr6*ecorr6+ftbis(3)*wturn4*eello_turn4+
+ & ftbis(2)*wturn3*eello_turn3+ftbis(5)*wturn6*eturn6+
+ & ftbis(2)*wel_loc*eel_loc+ftbis(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+#endif
+ weight=dexp(-betaT*(etot-potEmin)+entfac(t))
+#ifdef DEBUG
+ write (iout,*) "iparm",iparm," t",t," temper",temper,
+ & " etot",etot," entfac",entfac(t),
+ & " efree",etot-entfac(t)/betaT," potEmin",potEmin,
+ & " boltz",-betaT*(etot-potEmin)+entfac(t),
+ & " weight",weight," ebis",ebis
+#endif
+ etot=etot-temper*eprim
+#ifdef MPI
+ sumW_p(k,iparm)=sumW_p(k,iparm)+weight
+ sumE_p(k,iparm)=sumE_p(k,iparm)+etot*weight
+ sumEbis_p(k,iparm)=sumEbis_p(k,iparm)+ebis*weight
+ sumEsq_p(k,iparm)=sumEsq_p(k,iparm)+etot**2*weight
+ do j=1,nQ+2
+ sumQ_p(j,k,iparm)=sumQ_p(j,k,iparm)+q(j,t)*weight
+ sumQsq_p(j,k,iparm)=sumQsq_p(j,k,iparm)+q(j,t)**2*weight
+ sumEQ_p(j,k,iparm)=sumEQ_p(j,k,iparm)
+ & +etot*q(j,t)*weight
+ enddo
+#else
+ sumW(k,iparm)=sumW(k,iparm)+weight
+ sumE(k,iparm)=sumE(k,iparm)+etot*weight
+ sumEbis(k,iparm)=sumEbis(k,iparm)+ebis*weight
+ sumEsq(k,iparm)=sumEsq(k,iparm)+etot**2*weight
+ do j=1,nQ+2
+ sumQ(j,k,iparm)=sumQ(j,k,iparm)+q(j,t)*weight
+ sumQsq(j,k,iparm)=sumQsq(j,k,iparm)+q(j,t)**2*weight
+ sumEQ(j,k,iparm)=sumEQ(j,k,iparm)
+ & +etot*q(j,t)*weight
+ enddo
+#endif
+ enddo
+ indE = aint(potE(t,iparm)-aint(potEmin))
+ if (indE.ge.0 .and. indE.le.maxinde) then
+ if (indE.gt.upindE_p) upindE_p=indE
+ histE_p(indE)=histE_p(indE)+dexp(-entfac(t))
+ endif
+#ifdef MPI
+ do ib=1,nT_h(iparm)
+ potEmin=potEmin_all(ib,iparm)
+ expfac=dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ hfin_p(ind,ib)=hfin_p(ind,ib)+
+ & dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ if (rmsrgymap) then
+ indrgy=dint((q(nQ+2,t)-rgymin)/deltrgy)
+ indrms=dint((q(nQ+1,t)-rmsmin)/deltrms)
+ hrmsrgy_p(indrgy,indrms,ib)=
+ & hrmsrgy_p(indrgy,indrms,ib)+expfac
+ endif
+ enddo
+#else
+ do ib=1,nT_h(iparm)
+ potEmin=potEmin_all(ib,iparm)
+ expfac=dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ hfin(ind,ib)=hfin(ind,ib)+
+ & dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ if (rmsrgymap) then
+ indrgy=dint((q(nQ+2,t)-rgymin)/deltrgy)
+ indrms=dint((q(nQ+1,t)-rmsmin)/deltrms)
+ hrmsrgy(indrgy,indrms,ib)=
+ & hrmsrgy(indrgy,indrms,ib)+expfac
+ endif
+ enddo
+#endif
+ enddo ! t
+ do ib=1,nT_h(iparm)
+ if (histout) call MPI_Reduce(hfin_p(0,ib),hfin(0,ib),nbin,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ if (rmsrgymap) then
+ call MPI_Reduce(hrmsrgy_p(0,0,ib),hrmsrgy(0,0,ib),
+ & (MaxBinRgy+1)*(nbin_rms+1),MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ endif
+ enddo
+ call MPI_Reduce(upindE_p,upindE,1,
+ & MPI_INTEGER,MPI_MAX,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(histE_p(0),histE(0),maxindE,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+
+ if (me1.eq.master) then
+
+ if (histout) then
+
+ write (iout,'(6x,$)')
+ write (iout,'(f20.2,$)') (1.0d0/(1.987D-3*beta_h(ib,iparm)),
+ & ib=1,nT_h(iparm))
+ write (iout,*)
+
+ write (iout,'(/a)') 'Final histograms'
+ if (histfile) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//'.hist'
+ else
+ histname=prefix(:ilen(prefix))//'.hist'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//
+ & '_slice_'//licz2//'.hist'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.hist'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ endif
+
+ do t=0,tmax
+ liczba=t
+ sumH=0.0d0
+ do ib=1,nT_h(iparm)
+ sumH=sumH+hfin(t,ib)
+ enddo
+ if (sumH.gt.0.0d0) then
+ do j=1,nQ
+ jj = mod(liczba,nbin1)
+ liczba=liczba/nbin1
+ write (iout,'(f6.3,$)') dmin+(jj+0.5d0)*delta
+ if (histfile)
+ & write (ihist,'(f6.3,$)') dmin+(jj+0.5d0)*delta
+ enddo
+ do ib=1,nT_h(iparm)
+ write (iout,'(e20.10,$)') hfin(t,ib)
+ if (histfile) write (ihist,'(e20.10,$)') hfin(t,ib)
+ enddo
+ write (iout,'(i5)') iparm
+ if (histfile) write (ihist,'(i5)') iparm
+ endif
+ enddo
+
+ endif
+
+ if (entfile) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//"_par"//licz3//'.ent'
+ else
+ histname=prefix(:ilen(prefix))//'.ent'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'par_'//licz3//
+ & '_slice_'//licz2//'.ent'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.ent'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ write (ihist,'(a)') "# Microcanonical entropy"
+ do i=0,upindE
+ write (ihist,'(f8.0,$)') dint(potEmin)+i
+ if (histE(i).gt.0.0e0) then
+ write (ihist,'(f15.5,$)') dlog(histE(i))
+ else
+ write (ihist,'(f15.5,$)') 0.0d0
+ endif
+ enddo
+ write (ihist,*)
+ close(ihist)
+ endif
+ write (iout,*) "Microcanonical entropy"
+ do i=0,upindE
+ write (iout,'(f8.0,$)') dint(potEmin)+i
+ if (histE(i).gt.0.0e0) then
+ write (iout,'(f15.5,$)') dlog(histE(i))
+ else
+ write (iout,'(f15.5,$)') 0.0d0
+ endif
+ write (iout,*)
+ enddo
+ if (rmsrgymap) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//'.rmsrgy'
+ else
+ histname=prefix(:ilen(prefix))//'.rmsrgy'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//
+ & '_slice_'//licz2//'.rmsrgy'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.rmsrgy'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ do i=0,nbin_rms
+ do j=0,nbin_rgy
+ write(ihist,'(2f8.2,$)')
+ & rgymin+deltrgy*j,rmsmin+deltrms*i
+ do ib=1,nT_h(iparm)
+ if (hrmsrgy(j,i,ib).gt.0.0d0) then
+ write(ihist,'(e14.5,$)')
+ & -dlog(hrmsrgy(j,i,ib))/beta_h(ib,iparm)
+ & +potEmin
+ else
+ write(ihist,'(e14.5,$)') 1.0d6
+ endif
+ enddo
+ write (ihist,'(i2)') iparm
+ enddo
+ enddo
+ close(ihist)
+ endif
+ endif
+ enddo ! iparm
+#ifdef MPI
+ call MPI_Reduce(hfin_ent_p(0),hfin_ent(0),nbin,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumW_p(0,1),sumW(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumE_p(0,1),sumE(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEbis_p(0,1),sumEbis(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEsq_p(0,1),sumEsq(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumQ_p(1,0,1),sumQ(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Reduce(sumQsq_p(1,0,1),sumQsq(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEQ_p(1,0,1),sumEQ(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ if (me.eq.master) then
+#endif
+ write (iout,'(/a)') 'Thermal characteristics of folding'
+ if (nslice.eq.1) then
+ nazwa=prefix
+ else
+ nazwa=prefix(:ilen(prefix))//"_slice_"//licz2
+ endif
+ iln=ilen(nazwa)
+ if (nparmset.eq.1 .and. .not.separate_parset) then
+ nazwa=nazwa(:iln)//".thermal"
+ else if (nparmset.eq.1 .and. separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ nazwa=nazwa(:iln)//"_par_"//licz3//".thermal"
+ endif
+ do iparm=1,nParmSet
+ if (nparmset.gt.1) then
+ write(licz3,"(bz,i3.3)") iparm
+ nazwa=nazwa(:iln)//"_par_"//licz3//".thermal"
+ endif
+ open(34,file=nazwa)
+ if (separate_parset) then
+ write (iout,'(a,i3)') "Parameter set",myparm
+ else
+ write (iout,'(a,i3)') "Parameter set",iparm
+ endif
+ do i=0,NGridT
+ betaT=1.0d0/(1.987D-3*(startGridT+i*delta_T))
+ if (betaT.ge.beta_h(1,iparm)) then
+ potEmin=potEmin_all(1,iparm)
+ else if (betaT.lt.beta_h(nT_h(iparm),iparm)) then
+ potEmin=potEmin_all(nT_h(iparm),iparm)
+ else
+ do l=1,nT_h(iparm)-1
+ if (betaT.le.beta_h(l,iparm) .and.
+ & betaT.gt.beta_h(l+1,iparm)) then
+ potEmin=potEmin_all(l,iparm)
+ exit
+ endif
+ enddo
+ endif
+ sumE(i,iparm)=sumE(i,iparm)/sumW(i,iparm)
+ sumEbis(i,iparm)=(startGridT+i*delta_T)*sumEbis(i,iparm)/
+ & sumW(i,iparm)
+ sumEsq(i,iparm)=(sumEsq(i,iparm)/sumW(i,iparm)
+ & -sumE(i,iparm)**2)/(1.987D-3*(startGridT+i*delta_T)**2)
+ do j=1,nQ+2
+ sumQ(j,i,iparm)=sumQ(j,i,iparm)/sumW(i,iparm)
+ sumQsq(j,i,iparm)=sumQsq(j,i,iparm)/sumW(i,iparm)
+ & -sumQ(j,i,iparm)**2
+ sumEQ(j,i,iparm)=sumEQ(j,i,iparm)/sumW(i,iparm)
+ & -sumQ(j,i,iparm)*sumE(i,iparm)
+ enddo
+ sumW(i,iparm)=-dlog(sumW(i,iparm))*(1.987D-3*
+ & (startGridT+i*delta_T))+potEmin
+ write (iout,'(f7.1,2f15.5,$)') startGridT+i*delta_T,
+ & sumW(i,iparm),sumE(i,iparm)
+ write (iout,'(f10.5,$)') (sumQ(j,i,iparm),j=1,nQ+2)
+ write (iout,'(e15.5,$)') sumEsq(i,iparm)-sumEbis(i,iparm),
+ & (sumQsq(j,i,iparm),j=1,nQ+2),(sumEQ(j,i,iparm),j=1,nQ+2)
+ write (iout,*)
+ write (34,'(f7.1,2f15.5,$)') startGridT+i*delta_T,
+ & sumW(i,iparm),sumE(i,iparm)
+ write (34,'(f10.5,$)') (sumQ(j,i,iparm),j=1,nQ+2)
+ write (34,'(e15.5,$)') sumEsq(i,iparm)-sumEbis(i,iparm),
+ & (sumQsq(j,i,iparm),j=1,nQ+2),(sumEQ(j,i,iparm),j=1,nQ+2)
+ write (34,*)
+ enddo
+ close(34)
+ enddo
+ if (histout) then
+ do t=0,tmax
+ if (hfin_ent(t).gt.0.0d0) then
+ liczba=t
+ jj = mod(liczba,nbin1)
+ write (iout,'(f6.3,e20.10," ent")') dmin+(jj+0.5d0)*delta,
+ & hfin_ent(t)
+ if (histfile) write (ihist,'(f6.3,e20.10," ent")')
+ & dmin+(jj+0.5d0)*delta,
+ & hfin_ent(t)
+ endif
+ enddo
+ if (histfile) close(ihist)
+ endif
+
+#ifdef ZSCORE
+! Write data for zscore
+ if (nslice.eq.1) then
+ zscname=prefix(:ilen(prefix))//".zsc"
+ else
+ zscname=prefix(:ilen(prefix))//"_slice_"//licz2//".zsc"
+ endif
+#if defined(AIX) || defined(PGI)
+ open (izsc,file=prefix(:ilen(prefix))//'.zsc',position='append')
+#else
+ open (izsc,file=prefix(:ilen(prefix))//'.zsc',access='append')
+#endif
+ write (izsc,'("NQ=",i1," NPARM=",i1)') nQ,nParmSet
+ do iparm=1,nParmSet
+ write (izsc,'("NT=",i1)') nT_h(iparm)
+ do ib=1,nT_h(iparm)
+ write (izsc,'("TEMP=",f6.1," NR=",i2," SNK=",$)')
+ & 1.0d0/(beta_h(ib,iparm)*1.987D-3),nR(ib,iparm)
+ jj = min0(nR(ib,iparm),7)
+ write (izsc,'(i8,$)') (snk(i,ib,iparm,islice),i=1,jj)
+ write (izsc,'(a1,$)') (" ",i=22+8*jj+1,79)
+ write (izsc,'("&")')
+ if (nR(ib,iparm).gt.7) then
+ do ii=8,nR(ib,iparm),9
+ jj = min0(nR(ib,iparm),ii+8)
+ write (izsc,'(i8,$)') (snk(i,ib,iparm,islice),i=ii,jj)
+ write (izsc,'(a1,$') (" ",i=(jj-ii+1)*8+1,79)
+ write (izsc,'("&")')
+ enddo
+ endif
+ write (izsc,'("FI=",$)')
+ jj=min0(nR(ib,iparm),7)
+ write (izsc,'(f10.5,$)') (fi(i,ib,iparm),i=1,jj)
+ write (izsc,'(a1,$)') (" ",i=3+10*jj+1,79)
+ write (izsc,'("&")')
+ if (nR(ib,iparm).gt.7) then
+ do ii=8,nR(ib,iparm),9
+ jj = min0(nR(ib,iparm),ii+8)
+ write (izsc,'(f10.5,$)') (fi(i,ib,iparm),i=ii,jj)
+ if (jj.eq.nR(ib,iparm)) then
+ write (izsc,*)
+ else
+ write (izsc,'(a1,$)') (" ",i=10*(jj-ii+1)+1,79)
+ write (izsc,'(t80,"&")')
+ endif
+ enddo
+ endif
+ do i=1,nR(ib,iparm)
+ write (izsc,'("KH=",$)')
+ write (izsc,'(f7.2,$)') (Kh(j,i,ib,iparm),j=1,nQ)
+ write (izsc,'(" Q0=",$)')
+ write (izsc,'(f7.5,$)') (q0(j,i,ib,iparm),j=1,nQ)
+ write (izsc,*)
+ enddo
+ enddo
+ enddo
+ close(izsc)
+#endif
+#ifdef MPI
+ endif
+#endif
+
+ return
+ end
--- /dev/null
+ subroutine WHAM_CALC(islice,*)
+! Weighed Histogram Analysis Method (WHAM) code
+! Written by A. Liwo based on the work of Kumar et al.,
+! J.Comput.Chem., 13, 1011 (1992)
+!
+! 2/1/05 Multiple temperatures allowed.
+! 2/2/05 Free energies calculated directly from data points
+! acc. to Eq. (21) of Kumar et al.; final histograms also
+! constructed based on this equation.
+! 2/12/05 Multiple parameter sets included
+!
+! 2/2/05 Parallel version
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ integer nGridT
+ parameter (NGridT=400)
+ integer MaxBinRms,MaxBinRgy
+ parameter (MaxBinRms=100,MaxBinRgy=100)
+ integer MaxHdim
+c parameter (MaxHdim=200000)
+ parameter (MaxHdim=200)
+ integer maxinde
+ parameter (maxinde=200)
+#ifdef MPI
+ include "mpif.h"
+ include "COMMON.MPI"
+ integer ierror,errcode,status(MPI_STATUS_SIZE)
+#endif
+ include "COMMON.CONTROL"
+ include "COMMON.IOUNITS"
+ include "COMMON.FREE"
+ include "COMMON.ENERGIES"
+ include "COMMON.FFIELD"
+ include "COMMON.SBRIDGE"
+ include "COMMON.PROT"
+ include "COMMON.ENEPS"
+ integer MaxPoint,MaxPointProc
+ parameter (MaxPoint=MaxStr,
+ & MaxPointProc=MaxStr_Proc)
+ double precision finorm_max,potfac,entmin,entmax,expfac,vf
+ parameter (finorm_max=1.0d0)
+ integer islice
+ integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln
+ integer start,end,iharm,ib,iib,nbin1,nbin,nbin_rms,nbin_rgy,
+ & nbin_rmsrgy,liczba,iparm,nFi,indrgy,indrms
+ integer htot(0:MaxHdim),histent(0:2000)
+ double precision v(MaxPointProc,MaxR,MaxT_h,Max_Parm)
+ double precision energia(0:max_ene)
+#ifdef MPI
+ integer tmax_t,upindE_p
+ double precision fi_p(MaxR,MaxT_h,Max_Parm)
+ double precision sumW_p(0:nGridT,Max_Parm),
+ & sumE_p(0:nGridT,Max_Parm),sumEsq_p(0:nGridT,Max_Parm),
+ & sumQ_p(MaxQ1,0:nGridT,Max_Parm),
+ & sumQsq_p(MaxQ1,0:nGridT,Max_Parm),
+ & sumEQ_p(MaxQ1,0:nGridT,Max_Parm),
+ & sumEprim_p(MaxQ1,0:nGridT,Max_Parm),
+ & sumEbis_p(0:nGridT,Max_Parm)
+ double precision hfin_p(0:MaxHdim,maxT_h),
+ & hfin_ent_p(0:MaxHdim),histE_p(0:maxindE),sumH,
+ & hrmsrgy_p(0:MaxBinRgy,0:MaxBinRms,maxT_h)
+ double precision rgymin_t,rmsmin_t,rgymax_t,rmsmax_t
+ double precision potEmin_t,entmin_p,entmax_p
+ integer histent_p(0:2000)
+ logical lprint /.true./
+#endif
+ double precision delta_T /1.0d0/
+ double precision rgymin,rmsmin,rgymax,rmsmax
+ double precision sumW(0:NGridT,Max_Parm),sumE(0:NGridT,Max_Parm),
+ & sumEsq(0:NGridT,Max_Parm),sumQ(MaxQ1,0:NGridT,Max_Parm),
+ & sumQsq(MaxQ1,0:NGridT,Max_Parm),sumEQ(MaxQ1,0:NGridT,Max_Parm),
+ & sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT,
+ & weight,econstr
+ double precision fi(MaxR,maxT_h,Max_Parm),
+ & dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom,
+ & hfin(0:MaxHdim,maxT_h),histE(0:maxindE),
+ & hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h),
+ & potEmin,ent,
+ & hfin_ent(0:MaxHdim),vmax,aux
+ double precision fT(6),fTprim(6),fTbis(6),quot,quotl1,quotl,kfacl,
+ & eprim,ebis,temper,kfac/2.4d0/,T0/300.0d0/,startGridT/200.0d0/,
+ & eplus,eminus,logfac,tanhT,tt
+ double precision etot,evdw,evdw_t,evdw2,ees,evdw1,ebe,etors,
+ & escloc,ehpb,ecorr,ecorr5,ecorr6,eello_turn4,eello_turn3,
+ & eturn6,eel_loc,edihcnstr,etors_d,estr,evdw2_14,esccor
+
+ integer ind_point(maxpoint),upindE,indE
+ character*16 plik
+ character*1 licz1
+ character*2 licz2
+ character*3 licz3
+ character*128 nazwa
+ integer ilen
+ external ilen
+
+ write(licz2,'(bz,i2.2)') islice
+ nbin1 = 1.0d0/delta
+ write (iout,'(//80(1h-)/"Solving WHAM equations for slice",
+ & i2/80(1h-)//)') islice
+ write (iout,*) "delta",delta," nbin1",nbin1
+ write (iout,*) "MaxN",MaxN," MaxQ",MaxQ," MaHdim",MaxHdim
+ call flush(iout)
+ dmin=0.0d0
+ tmax=0
+ potEmin=1.0d10
+ rgymin=1.0d10
+ rmsmin=1.0d10
+ rgymax=0.0d0
+ rmsmax=0.0d0
+ do t=0,MaxN
+ htot(t)=0
+ enddo
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+ do j=1,nParmSet
+ if (potE(i,j).le.potEmin) potEmin=potE(i,j)
+ enddo
+ if (q(nQ+1,i).lt.rmsmin) rmsmin=q(nQ+1,i)
+ if (q(nQ+1,i).gt.rmsmax) rmsmax=q(nQ+1,i)
+ if (q(nQ+2,i).lt.rgymin) rgymin=q(nQ+2,i)
+ if (q(nQ+2,i).gt.rgymax) rgymax=q(nQ+2,i)
+ ind_point(i)=0
+ do j=nQ,1,-1
+ ind=(q(j,i)-dmin+1.0d-8)/delta
+ if (j.eq.1) then
+ ind_point(i)=ind_point(i)+ind
+ else
+ ind_point(i)=ind_point(i)+nbin1**(j-1)*ind
+ endif
+c write (iout,*) "i",i," j",j," q",q(j,i)," ind_point",
+c & ind_point(i)
+ call flush(iout)
+ if (ind_point(i).lt.0 .or. ind_point(i).gt.MaxHdim) then
+ write (iout,*) "Error - index exceeds range for point",i,
+ & " q=",q(j,i)," ind",ind_point(i)
+#ifdef MPI
+ write (iout,*) "Processor",me1
+ call flush(iout)
+ call MPI_Abort(MPI_COMM_WORLD, Ierror, Errcode )
+#endif
+ stop
+ endif
+ enddo ! j
+ if (ind_point(i).gt.tmax) tmax=ind_point(i)
+ htot(ind_point(i))=htot(ind_point(i))+1
+#ifdef DEBUG
+ write (iout,*) "i",i,"q",(q(j,i),j=1,nQ)," ind",ind_point(i),
+ & " htot",htot(ind_point(i))
+ call flush(iout)
+#endif
+ enddo ! i
+ call flush(iout)
+
+ nbin=nbin1**nQ-1
+ write (iout,'(a)') "Numbers of counts in Q bins"
+ do t=0,tmax
+ if (htot(t).gt.0) then
+ write (iout,'(i15,$)') t
+ liczba=t
+ do j=1,nQ
+ jj = mod(liczba,nbin1)
+ liczba=liczba/nbin1
+ write (iout,'(i5,$)') jj
+ enddo
+ write (iout,'(i8)') htot(t)
+ endif
+ enddo
+ do iparm=1,nParmSet
+ write (iout,'(a,i3)') "Number of data points for parameter set",
+ & iparm
+ write (iout,'(i7,$)') ((snk(m,ib,iparm,islice),m=1,nr(ib,iparm)),
+ & ib=1,nT_h(iparm))
+ write (iout,'(i8)') stot(islice)
+ write (iout,'(a)')
+ enddo
+ call flush(iout)
+
+#ifdef MPI
+ call MPI_AllReduce(tmax,tmax_t,1,MPI_INTEGER,MPI_MAX,
+ & WHAM_COMM,IERROR)
+ tmax=tmax_t
+ call MPI_AllReduce(potEmin,potEmin_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MIN,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rmsmin,rmsmin_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MIN,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rmsmax,rmsmax_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MAX,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rgymin,rgymin_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MIN,WHAM_COMM,IERROR)
+ call MPI_AllReduce(rgymax,rgymax_t,1,MPI_DOUBLE_PRECISION,
+ & MPI_MAX,WHAM_COMM,IERROR)
+ potEmin=potEmin_t/2
+ rgymin=rgymin_t
+ rgymax=rgymax_t
+ rmsmin=rmsmin_t
+ rmsmax=rmsmax_t
+ write (iout,*) "potEmin",potEmin
+#endif
+ rmsmin=deltrms*dint(rmsmin/deltrms)
+ rmsmax=deltrms*dint(rmsmax/deltrms)
+ rgymin=deltrms*dint(rgymin/deltrgy)
+ rgymax=deltrms*dint(rgymax/deltrgy)
+ nbin_rms=(rmsmax-rmsmin)/deltrms
+ nbin_rgy=(rgymax-rgymin)/deltrgy
+ write (iout,*) "rmsmin",rmsmin," rmsmax",rmsmax," rgymin",rgymin,
+ & " rgymax",rgymax," nbin_rms",nbin_rms," nbin_rgy",nbin_rgy
+ nFi=0
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ nFi=nFi+nR(j,i)
+ enddo
+ enddo
+ write (iout,*) "nFi",nFi
+! Compute the Boltzmann factor corresponing to restrain potentials in different
+! simulations.
+#ifdef MPI
+ do i=1,scount(me1)
+#else
+ do i=1,ntot(islice)
+#endif
+c write (9,'(3i5,f10.5)') i,(iparm,potE(i,iparm),iparm=1,nParmSet)
+ do iparm=1,nParmSet
+#ifdef DEBUG
+ write (iout,'(2i5,21f8.2)') i,iparm,
+ & (enetb(k,i,iparm),k=1,21)
+#endif
+ call restore_parm(iparm)
+#ifdef DEBUG
+ write (iout,*) wsc,wscp,welec,wvdwpp,wang,wtor,wscloc,
+ & wcorr,wcorr5,wcorr6,wturn4,wturn3,wturn6,wel_loc,
+ & wtor_d,wsccor,wbond
+#endif
+ do ib=1,nT_h(iparm)
+ if (rescale_mode.eq.1) then
+ quot=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ fT(l)=kfacl/(kfacl-1.0d0+quotl)
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+ else if (rescale_mode.eq.2) then
+ quot=1.0d0/(T0*beta_h(ib,iparm)*1.987D-3)
+ quotl=1.0d0
+ do l=1,5
+ quotl=quotl*quot
+ fT(l)=1.12692801104297249644d0/
+ & dlog(dexp(quotl)+dexp(-quotl))
+ enddo
+#if defined(FUNCTH)
+ tt = 1.0d0/(beta_h(ib,iparm)*1.987D-3)
+ ft(6)=(320.0d0+80.0d0*dtanh((tt-320.0d0)/80.0d0))/320.0d0
+#elif defined(FUNCT)
+ ft(6)=1.0d0/(beta_h(ib,iparm)*1.987D-3*T0)
+#else
+ ft(6)=1.0d0
+#endif
+c write (iout,*) 1.0d0/(beta_h(ib,iparm)*1.987D-3),ft
+ else if (rescale_mode.eq.0) then
+ do l=1,6
+ fT(l)=1.0d0
+ enddo
+ else
+ write (iout,*) "Error in WHAM_CALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+ evdw=enetb(1,i,iparm)
+ evdw_t=enetb(21,i,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,i,iparm)
+ evdw2=enetb(2,i,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,i,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,i,iparm)
+ evdw1=enetb(16,i,iparm)
+#else
+ ees=enetb(3,i,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,i,iparm)
+ ecorr5=enetb(5,i,iparm)
+ ecorr6=enetb(6,i,iparm)
+ eel_loc=enetb(7,i,iparm)
+ eello_turn3=enetb(8,i,iparm)
+ eello_turn4=enetb(9,i,iparm)
+ eturn6=enetb(10,i,iparm)
+ ebe=enetb(11,i,iparm)
+ escloc=enetb(12,i,iparm)
+ etors=enetb(13,i,iparm)
+ etors_d=enetb(14,i,iparm)
+ ehpb=enetb(15,i,iparm)
+ estr=enetb(18,i,iparm)
+ esccor=enetb(19,i,iparm)
+ edihcnstr=enetb(20,i,iparm)
+#ifdef DEBUG
+ write (iout,'(3i5,6f5.2,14f12.3)') i,ib,iparm,(ft(l),l=1,6),
+ & evdw+evdw_t,evdw2,ees,evdw1,ecorr,eel_loc,estr,ebe,escloc,
+ & etors,etors_d,eello_turn3,eello_turn4,esccor
+#endif
+
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+#endif
+#ifdef DEBUG
+ write (iout,*) i,iparm,1.0d0/(beta_h(ib,iparm)*1.987D-3),
+ & etot,potEmin
+#endif
+#ifdef DEBUG
+ if (iparm.eq.1 .and. ib.eq.1) then
+ write (iout,*)"Conformation",i
+ energia(0)=etot
+ do k=1,max_ene
+ energia(k)=enetb(k,i,iparm)
+ enddo
+ call enerprint(energia(0),fT)
+ endif
+#endif
+ do kk=1,nR(ib,iparm)
+ Econstr=0.0d0
+ do j=1,nQ
+ dd = q(j,i)
+ Econstr=Econstr+Kh(j,kk,ib,iparm)
+ & *(dd-q0(j,kk,ib,iparm))**2
+ enddo
+ v(i,kk,ib,iparm)=
+ & -beta_h(ib,iparm)*(etot-potEmin+Econstr)
+#ifdef DEBUG
+ write (iout,'(4i5,4e15.5)') i,kk,ib,iparm,
+ & etot,potEmin,etot-potEmin,v(i,kk,ib,iparm)
+#endif
+ enddo ! kk
+ enddo ! ib
+ enddo ! iparm
+ enddo ! i
+! Simple iteration to calculate free energies corresponding to all simulation
+! runs.
+ do iter=1,maxit
+
+! Compute new free-energy values corresponding to the righ-hand side of the
+! equation and their derivatives.
+ write (iout,*) "------------------------fi"
+#ifdef MPI
+ do t=1,scount(me1)
+#else
+ do t=1,ntot(islice)
+#endif
+ vmax=-1.0d+20
+ do i=1,nParmSet
+ do k=1,nT_h(i)
+ do l=1,nR(k,i)
+ vf=v(t,l,k,i)+f(l,k,i)
+ if (vf.gt.vmax) vmax=vf
+ enddo
+ enddo
+ enddo
+ denom=0.0d0
+ do i=1,nParmSet
+ do k=1,nT_h(i)
+ do l=1,nR(k,i)
+ aux=f(l,k,i)+v(t,l,k,i)-vmax
+ if (aux.gt.-200.0d0)
+ & denom=denom+snk(l,k,i,islice)*dexp(aux)
+ enddo
+ enddo
+ enddo
+ entfac(t)=-dlog(denom)-vmax
+#ifdef DEBUG
+ write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t)
+#endif
+ enddo
+ do iparm=1,nParmSet
+ do iib=1,nT_h(iparm)
+ do ii=1,nR(iib,iparm)
+#ifdef MPI
+ fi_p(ii,iib,iparm)=0.0d0
+ do t=1,scount(me)
+ fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm)
+ & +dexp(v(t,ii,iib,iparm)+entfac(t))
+#ifdef DEBUG
+ write (iout,'(4i5,3e15.5)') t,ii,iib,iparm,
+ & v(t,ii,iib,iparm),entfac(t),fi_p(ii,iib,iparm)
+#endif
+ enddo
+#else
+ fi(ii,iib,iparm)=0.0d0
+ do t=1,ntot(islice)
+ fi(ii,iib,iparm)=fi(ii,iib,iparm)
+ & +dexp(v(t,ii,iib,iparm)+entfac(t))
+ enddo
+#endif
+ enddo ! ii
+ enddo ! iib
+ enddo ! iparm
+
+#ifdef MPI
+#ifdef DEBUG
+ write (iout,*) "fi before MPI_Reduce me",me,' master',master
+ do iparm=1,nParmSet
+ do ib=1,nT_h(nparmset)
+ write (iout,*) "iparm",iparm," ib",ib
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ write (iout,'(8e15.5)') (fi_p(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+#endif
+ write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet,
+ & maxR*MaxT_h*nParmSet
+ write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
+ & " WHAM_COMM",WHAM_COMM
+ call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,
+ & MPI_SUM,Master,WHAM_COMM,IERROR)
+#ifdef DEBUG
+ write (iout,*) "fi after MPI_Reduce nparmset",nparmset
+ do iparm=1,nParmSet
+ write (iout,*) "iparm",iparm
+ do ib=1,nT_h(iparm)
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ write (iout,'(8e15.5)') (fi(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+#endif
+ if (me1.eq.Master) then
+#endif
+ avefi=0.0d0
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))
+ avefi=avefi+fi(i,ib,iparm)
+ enddo
+ enddo
+ enddo
+ avefi=avefi/nFi
+ do iparm=1,nParmSet
+ write (iout,*) "Parameter set",iparm
+ do ib =1,nT_h(iparm)
+ write (iout,*) "beta=",beta_h(ib,iparm)
+ do i=1,nR(ib,iparm)
+ fi(i,ib,iparm)=fi(i,ib,iparm)-avefi
+ enddo
+ write (iout,'(8f10.5)') (fi(i,ib,iparm),i=1,nR(ib,iparm))
+ write (iout,'(8f10.5)') (f(i,ib,iparm),i=1,nR(ib,iparm))
+ enddo
+ enddo
+
+! Compute the norm of free-energy increments.
+ finorm=0.0d0
+ do iparm=1,nParmSet
+ do ib=1,nT_h(iparm)
+ do i=1,nR(ib,iparm)
+ finorm=finorm+dabs(fi(i,ib,iparm)-f(i,ib,iparm))
+ f(i,ib,iparm)=fi(i,ib,iparm)
+ enddo
+ enddo
+ enddo
+
+ write (iout,*) 'Iteration',iter,' finorm',finorm
+
+#ifdef MPI
+ endif
+ call MPI_Bcast(f(1,1,1),MaxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Bcast(finorm,1,MPI_DOUBLE_PRECISION,Master,
+ & WHAM_COMM,IERROR)
+#endif
+! Exit, if the increment norm is smaller than pre-assigned tolerance.
+ if (finorm.lt.fimin) then
+ write (iout,*) 'Iteration converged'
+ goto 20
+ endif
+
+ enddo ! iter
+
+ 20 continue
+! Now, put together the histograms from all simulations, in order to get the
+! unbiased total histogram.
+#ifdef MPI
+ do t=0,tmax
+ hfin_ent_p(t)=0.0d0
+ enddo
+#else
+ do t=0,tmax
+ hfin_ent(t)=0.0d0
+ enddo
+#endif
+ write (iout,*) "--------------hist"
+#ifdef MPI
+ do iparm=1,nParmSet
+ do i=0,nGridT
+ sumW_p(i,iparm)=0.0d0
+ sumE_p(i,iparm)=0.0d0
+ sumEbis_p(i,iparm)=0.0d0
+ sumEsq_p(i,iparm)=0.0d0
+ do j=1,nQ+2
+ sumQ_p(j,i,iparm)=0.0d0
+ sumQsq_p(j,i,iparm)=0.0d0
+ sumEQ_p(j,i,iparm)=0.0d0
+ enddo
+ enddo
+ enddo
+ upindE_p=0
+#else
+ do iparm=1,nParmSet
+ do i=0,nGridT
+ sumW(i,iparm)=0.0d0
+ sumE(i,iparm)=0.0d0
+ sumEbis(i,iparm)=0.0d0
+ sumEsq(i,iparm)=0.0d0
+ do j=1,nQ+2
+ sumQ(j,i,iparm)=0.0d0
+ sumQsq(j,i,iparm)=0.0d0
+ sumEQ(j,i,iparm)=0.0d0
+ enddo
+ enddo
+ enddo
+ upindE=0
+#endif
+c 8/26/05 entropy distribution
+#ifdef MPI
+ entmin_p=1.0d10
+ entmax_p=-1.0d10
+ do t=1,scount(me1)
+c ent=-dlog(entfac(t))
+ ent=entfac(t)
+ if (ent.lt.entmin_p) entmin_p=ent
+ if (ent.gt.entmax_p) entmax_p=ent
+ enddo
+ write (iout,*) "entmin",entmin_p," entmax",entmax_p
+ call flush(iout)
+ call MPI_Allreduce(entmin_p,entmin,1,MPI_DOUBLE_PRECISION,MPI_MIN,
+ & WHAM_COMM,IERROR)
+ call MPI_Allreduce(entmax_p,entmax,1,MPI_DOUBLE_PRECISION,MPI_MAX,
+ & WHAM_COMM,IERROR)
+ ientmax=entmax-entmin
+ if (ientmax.gt.2000) ientmax=2000
+ write (iout,*) "entmin",entmin," entmax",entmax," ientmax",ientmax
+ call flush(iout)
+ do t=1,scount(me1)
+c ient=-dlog(entfac(t))-entmin
+ ient=entfac(t)-entmin
+ if (ient.le.2000) histent_p(ient)=histent_p(ient)+1
+ enddo
+ call MPI_Allreduce(histent_p(0),histent(0),ientmax+1,MPI_INTEGER,
+ & MPI_SUM,WHAM_COMM,IERROR)
+ if (me1.eq.Master) then
+ write (iout,*) "Entropy histogram"
+ do i=0,ientmax
+ write(iout,'(f15.4,i10)') entmin+i,histent(i)
+ enddo
+ endif
+#else
+ entmin=1.0d10
+ entmax=-1.0d10
+ do t=1,ntot(islice)
+ ent=entfac(t)
+ if (ent.lt.entmin) entmin=ent
+ if (ent.gt.entmax) entmax=ent
+ enddo
+ ientmax=-dlog(entmax)-entmin
+ if (ientmax.gt.2000) ientmax=2000
+ do t=1,ntot(islice)
+ ient=entfac(t)-entmin
+ if (ient.le.2000) histent(ient)=histent(ient)+1
+ enddo
+ write (iout,*) "Entropy histogram"
+ do i=0,ientmax
+ write(iout,'(2f15.4)') entmin+i,histent(i)
+ enddo
+#endif
+
+#ifdef MPI
+c write (iout,*) "me1",me1," scount",scount(me1)
+
+ do iparm=1,nParmSet
+
+#ifdef MPI
+ do ib=1,nT_h(iparm)
+ do t=0,tmax
+ hfin_p(t,ib)=0.0d0
+ enddo
+ enddo
+ do i=1,maxindE
+ histE_p(i)=0.0d0
+ enddo
+#else
+ do ib=1,nT_h(iparm)
+ do t=0,tmax
+ hfin(t,ib)=0.0d0
+ enddo
+ enddo
+ do i=1,maxindE
+ histE(i)=0.0d0
+ enddo
+#endif
+ do ib=1,nT_h(iparm)
+ do i=0,MaxBinRms
+ do j=0,MaxBinRgy
+ hrmsrgy(j,i,ib)=0.0d0
+#ifdef MPI
+ hrmsrgy_p(j,i,ib)=0.0d0
+#endif
+ enddo
+ enddo
+ enddo
+
+ do t=1,scount(me1)
+#else
+ do t=1,ntot(islice)
+#endif
+ ind = ind_point(t)
+#ifdef MPI
+ hfin_ent_p(ind)=hfin_ent_p(ind)+dexp(entfac(t))
+#else
+ hfin_ent(ind)=hfin_ent(ind)+dexp(entfac(t))
+#endif
+c write (iout,'(2i5,20f8.2)') t,t,(enetb(k,t,iparm),k=1,18)
+ call restore_parm(iparm)
+ evdw=enetb(21,t,iparm)
+ evdw_t=enetb(1,t,iparm)
+#ifdef SCP14
+ evdw2_14=enetb(17,t,iparm)
+ evdw2=enetb(2,t,iparm)+evdw2_14
+#else
+ evdw2=enetb(2,t,iparm)
+ evdw2_14=0.0d0
+#endif
+#ifdef SPLITELE
+ ees=enetb(3,t,iparm)
+ evdw1=enetb(16,t,iparm)
+#else
+ ees=enetb(3,t,iparm)
+ evdw1=0.0d0
+#endif
+ ecorr=enetb(4,t,iparm)
+ ecorr5=enetb(5,t,iparm)
+ ecorr6=enetb(6,t,iparm)
+ eel_loc=enetb(7,t,iparm)
+ eello_turn3=enetb(8,t,iparm)
+ eello_turn4=enetb(9,t,iparm)
+ eturn6=enetb(10,t,iparm)
+ ebe=enetb(11,t,iparm)
+ escloc=enetb(12,t,iparm)
+ etors=enetb(13,t,iparm)
+ etors_d=enetb(14,t,iparm)
+ ehpb=enetb(15,t,iparm)
+ estr=enetb(18,t,iparm)
+ esccor=enetb(19,t,iparm)
+ edihcnstr=enetb(20,t,iparm)
+ edihcnstr=0.0d0
+ do k=0,nGridT
+ betaT=startGridT+k*delta_T
+ temper=betaT
+c fT=T0/betaT
+c ft=2*T0/(T0+betaT)
+ if (rescale_mode.eq.1) then
+ quot=betaT/T0
+ quotl=1.0d0
+ kfacl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ kfacl=kfacl*kfac
+ denom=kfacl-1.0d0+quotl
+ fT(l)=kfacl/denom
+ ftprim(l)=-l*ft(l)*quotl1/(T0*denom)
+ ftbis(l)=l*kfacl*quotl1*
+ & (2*l*quotl-(l-1)*denom)/(quot*t0*t0*denom**3)
+ enddo
+#if defined(FUNCTH)
+ ft(6)=(320.0d0+80.0d0*dtanh((betaT-320.0d0)/80.0d0))/
+ & 320.0d0
+ ftprim(6)=1.0d0/(320.0d0*dcosh((betaT-320.0d0)/80.0d0)**2)
+ ftbis(6)=-2.0d0*dtanh((betaT-320.0d0)/80.0d0)
+ & /(320.0d0*80.0d0*dcosh((betaT-320.0d0)/80.0d0)**3)
+#elif defined(FUNCT)
+ fT(6)=betaT/T0
+ ftprim(6)=1.0d0/T0
+ ftbis(6)=0.0d0
+#else
+ fT(6)=1.0d0
+ ftprim(6)=0.0d0
+ ftbis(6)=0.0d0
+#endif
+ else if (rescale_mode.eq.2) then
+ quot=betaT/T0
+ quotl=1.0d0
+ do l=1,5
+ quotl1=quotl
+ quotl=quotl*quot
+ eplus=dexp(quotl)
+ eminus=dexp(-quotl)
+ logfac=1.0d0/dlog(eplus+eminus)
+ tanhT=(eplus-eminus)/(eplus+eminus)
+ fT(l)=1.12692801104297249644d0*logfac
+ ftprim(l)=-l*quotl1*ft(l)*tanhT*logfac/T0
+ ftbis(l)=(l-1)*ftprim(l)/(quot*T0)-
+ & 2*l*quotl1/T0*logfac*
+ & (2*l*quotl1*ft(l)/(T0*(eplus+eminus)**2)
+ & +ftprim(l)*tanhT)
+ enddo
+#if defined(FUNCTH)
+ ft(6)=(320.0d0+80.0d0*dtanh((betaT-320.0d0)/80.0d0))/
+ & 320.0d0
+ ftprim(6)=1.0d0/(320.0d0*dcosh((betaT-320.0d0)/80.0d0)**2)
+ ftbis(6)=-2.0d0*dtanh((betaT-320.0d0)/80.0d0)
+ & /(320.0d0*80.0d0*dcosh((betaT-320.0d0)/80.0d0)**3)
+#elif defined(FUNCT)
+ fT(6)=betaT/T0
+ ftprim(6)=1.0d0/T0
+ ftbis(6)=0.0d0
+#else
+ fT(6)=1.0d0
+ ftprim(6)=0.0d0
+ ftbis(6)=0.0d0
+#endif
+ else if (rescale_mode.eq.0) then
+ do l=1,5
+ fT(l)=1.0d0
+ ftprim(l)=0.0d0
+ enddo
+ else
+ write (iout,*) "Error in WHAM_CALC: wrong RESCALE_MODE",
+ & rescale_mode
+ call flush(iout)
+ return1
+ endif
+c write (iout,*) "ftprim",ftprim
+c write (iout,*) "ftbis",ftbis
+ betaT=1.0d0/(1.987D-3*betaT)
+#ifdef SPLITELE
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2+ft(1)*welec*ees
+ & +wvdwpp*evdw1
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc
+ & +edihcnstr+ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+ eprim=ftprim(6)*evdw_t+ftprim(1)*welec*ees
+ & +ftprim(1)*wtor*etors+
+ & ftprim(3)*wcorr*ecorr+ftprim(4)*wcorr5*ecorr5+
+ & ftprim(5)*wcorr6*ecorr6+ftprim(3)*wturn4*eello_turn4+
+ & ftprim(2)*wturn3*eello_turn3+ftprim(5)*wturn6*eturn6+
+ & ftprim(2)*wel_loc*eel_loc+ftprim(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+ ebis=ftbis(1)*welec*ees+ftbis(1)*wtor*etors+
+ & ftbis(3)*wcorr*ecorr+ftbis(4)*wcorr5*ecorr5+
+ & ftbis(5)*wcorr6*ecorr6+ftbis(3)*wturn4*eello_turn4+
+ & ftbis(2)*wturn3*eello_turn3+ftbis(5)*wturn6*eturn6+
+ & ftbis(2)*wel_loc*eel_loc+ftbis(2)*wtor_d*etors_d+
+ & ftbis(1)*wsccor*esccor
+#else
+ etot=wsc*(evdw+ft(6)*evdw_t)+wscp*evdw2
+ & +ft(1)*welec*(ees+evdw1)
+ & +wang*ebe+ft(1)*wtor*etors+wscloc*escloc
+ & +wstrain*ehpb+nss*ebr+ft(3)*wcorr*ecorr+ft(4)*wcorr5*ecorr5
+ & +ft(5)*wcorr6*ecorr6+ft(3)*wturn4*eello_turn4
+ & +ft(2)*wturn3*eello_turn3
+ & +ft(5)*wturn6*eturn6+ft(2)*wel_loc*eel_loc+edihcnstr
+ & +ft(2)*wtor_d*etors_d+ft(1)*wsccor*esccor
+ & +wbond*estr
+ eprim=ftprim(6)*evdw_t+ftprim(1)*welec*(ees+evdw1)
+ & +ftprim(1)*wtor*etors+
+ & ftprim(3)*wcorr*ecorr+ftprim(4)*wcorr5*ecorr5+
+ & ftprim(5)*wcorr6*ecorr6+ftprim(3)*wturn4*eello_turn4+
+ & ftprim(2)*wturn3*eello_turn3+ftprim(5)*wturn6*eturn6+
+ & ftprim(2)*wel_loc*eel_loc+ftprim(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+ ebis=ftbis(1)*welec*(ees+evdw1)+ftbis(1)*wtor*etors+
+ & ftbis(3)*wcorr*ecorr+ftbis(4)*wcorr5*ecorr5+
+ & ftbis(5)*wcorr6*ecorr6+ftbis(3)*wturn4*eello_turn4+
+ & ftbis(2)*wturn3*eello_turn3+ftbis(5)*wturn6*eturn6+
+ & ftbis(2)*wel_loc*eel_loc+ftbis(2)*wtor_d*etors_d+
+ & ftprim(1)*wsccor*esccor
+#endif
+ weight=dexp(-betaT*(etot-potEmin)+entfac(t))
+#define DEBUG
+#ifdef DEBUG
+ write (iout,*) "iparm",iparm," t",t," betaT",betaT,
+ & " etot",etot," entfac",entfac(t),
+ & " weight",weight," ebis",ebis
+#endif
+#undef DEBUG
+ etot=etot-temper*eprim
+#ifdef MPI
+ sumW_p(k,iparm)=sumW_p(k,iparm)+weight
+ sumE_p(k,iparm)=sumE_p(k,iparm)+etot*weight
+ sumEbis_p(k,iparm)=sumEbis_p(k,iparm)+ebis*weight
+ sumEsq_p(k,iparm)=sumEsq_p(k,iparm)+etot**2*weight
+ do j=1,nQ+2
+ sumQ_p(j,k,iparm)=sumQ_p(j,k,iparm)+q(j,t)*weight
+ sumQsq_p(j,k,iparm)=sumQsq_p(j,k,iparm)+q(j,t)**2*weight
+ sumEQ_p(j,k,iparm)=sumEQ_p(j,k,iparm)
+ & +etot*q(j,t)*weight
+ enddo
+#else
+ sumW(k,iparm)=sumW(k,iparm)+weight
+ sumE(k,iparm)=sumE(k,iparm)+etot*weight
+ sumEbis(k,iparm)=sumEbis(k,iparm)+ebis*weight
+ sumEsq(k,iparm)=sumEsq(k,iparm)+etot**2*weight
+ do j=1,nQ+2
+ sumQ(j,k,iparm)=sumQ(j,k,iparm)+q(j,t)*weight
+ sumQsq(j,k,iparm)=sumQsq(j,k,iparm)+q(j,t)**2*weight
+ sumEQ(j,k,iparm)=sumEQ(j,k,iparm)
+ & +etot*q(j,t)*weight
+ enddo
+#endif
+ enddo
+ indE = aint(potE(t,iparm)-aint(potEmin))
+ if (indE.ge.0 .and. indE.le.maxinde) then
+ if (indE.gt.upindE_p) upindE_p=indE
+ histE_p(indE)=histE_p(indE)+dexp(-entfac(t))
+ endif
+#ifdef MPI
+ do ib=1,nT_h(iparm)
+ expfac=dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ hfin_p(ind,ib)=hfin_p(ind,ib)+
+ & dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ if (rmsrgymap) then
+ indrgy=dint((q(nQ+2,t)-rgymin)/deltrgy)
+ indrms=dint((q(nQ+1,t)-rmsmin)/deltrms)
+ hrmsrgy_p(indrgy,indrms,ib)=
+ & hrmsrgy_p(indrgy,indrms,ib)+expfac
+ endif
+ enddo
+#else
+ do ib=1,nT_h(iparm)
+ expfac=dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ hfin(ind,ib)=hfin(ind,ib)+
+ & dexp(-beta_h(ib,iparm)*(etot-potEmin)+entfac(t))
+ if (rmsrgymap) then
+ indrgy=dint((q(nQ+2,t)-rgymin)/deltrgy)
+ indrms=dint((q(nQ+1,t)-rmsmin)/deltrms)
+ hrmsrgy(indrgy,indrms,ib)=
+ & hrmsrgy(indrgy,indrms,ib)+expfac
+ endif
+ enddo
+#endif
+ enddo ! t
+ do ib=1,nT_h(iparm)
+ if (histout) call MPI_Reduce(hfin_p(0,ib),hfin(0,ib),nbin,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ if (rmsrgymap) then
+ call MPI_Reduce(hrmsrgy_p(0,0,ib),hrmsrgy(0,0,ib),
+ & (MaxBinRgy+1)*(nbin_rms+1),MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ endif
+ enddo
+ call MPI_Reduce(upindE_p,upindE,1,
+ & MPI_INTEGER,MPI_MAX,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(histE_p(0),histE(0),maxindE,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+
+ if (me1.eq.master) then
+
+ if (histout) then
+
+ write (iout,'(6x,$)')
+ write (iout,'(f20.2,$)') (1.0d0/(1.987D-3*beta_h(ib,iparm)),
+ & ib=1,nT_h(iparm))
+ write (iout,*)
+
+ write (iout,'(/a)') 'Final histograms'
+ if (histfile) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//'.hist'
+ else
+ histname=prefix(:ilen(prefix))//'.hist'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//
+ & '_slice_'//licz2//'.hist'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.hist'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ endif
+
+ do t=0,tmax
+ liczba=t
+ sumH=0.0d0
+ do ib=1,nT_h(iparm)
+ sumH=sumH+hfin(t,ib)
+ enddo
+ if (sumH.gt.0.0d0) then
+ do j=1,nQ
+ jj = mod(liczba,nbin1)
+ liczba=liczba/nbin1
+ write (iout,'(f6.3,$)') dmin+(jj+0.5d0)*delta
+ if (histfile)
+ & write (ihist,'(f6.3,$)') dmin+(jj+0.5d0)*delta
+ enddo
+ do ib=1,nT_h(iparm)
+ write (iout,'(e20.10,$)') hfin(t,ib)
+ if (histfile) write (ihist,'(e20.10,$)') hfin(t,ib)
+ enddo
+ write (iout,'(i5)') iparm
+ if (histfile) write (ihist,'(i5)') iparm
+ endif
+ enddo
+
+ endif
+
+ if (entfile) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//"_par"//licz3//'.ent'
+ else
+ histname=prefix(:ilen(prefix))//'.ent'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'par_'//licz3//
+ & '_slice_'//licz2//'.ent'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.ent'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ write (ihist,'(a)') "# Microcanonical entropy"
+ do i=0,upindE
+ write (ihist,'(f8.0,$)') dint(potEmin)+i
+ if (histE(i).gt.0.0e0) then
+ write (ihist,'(f15.5,$)') dlog(histE(i))
+ else
+ write (ihist,'(f15.5,$)') 0.0d0
+ endif
+ enddo
+ write (ihist,*)
+ close(ihist)
+ endif
+ write (iout,*) "Microcanonical entropy"
+ do i=0,upindE
+ write (iout,'(f8.0,$)') dint(potEmin)+i
+ if (histE(i).gt.0.0e0) then
+ write (iout,'(f15.5,$)') dlog(histE(i))
+ else
+ write (iout,'(f15.5,$)') 0.0d0
+ endif
+ write (iout,*)
+ enddo
+ if (rmsrgymap) then
+ if (nslice.eq.1) then
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//'.rmsrgy'
+ else
+ histname=prefix(:ilen(prefix))//'.rmsrgy'
+ endif
+ else
+ if (separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ histname=prefix(:ilen(prefix))//'_par'//licz3//
+ & '_slice_'//licz2//'.rmsrgy'
+ else
+ histname=prefix(:ilen(prefix))//'_slice_'//licz2//'.rmsrgy'
+ endif
+ endif
+#if defined(AIX) || defined(PGI)
+ open (ihist,file=histname,position='append')
+#else
+ open (ihist,file=histname,access='append')
+#endif
+ do i=0,nbin_rms
+ do j=0,nbin_rgy
+ write(ihist,'(2f8.2,$)')
+ & rgymin+deltrgy*j,rmsmin+deltrms*i
+ do ib=1,nT_h(iparm)
+ if (hrmsrgy(j,i,ib).gt.0.0d0) then
+ write(ihist,'(e14.5,$)')
+ & -dlog(hrmsrgy(j,i,ib))/beta_h(ib,iparm)
+ & +potEmin
+ else
+ write(ihist,'(e14.5,$)') 1.0d6
+ endif
+ enddo
+ write (ihist,'(i2)') iparm
+ enddo
+ enddo
+ close(ihist)
+ endif
+ endif
+ enddo ! iparm
+#ifdef MPI
+ call MPI_Reduce(hfin_ent_p(0),hfin_ent(0),nbin,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumW_p(0,1),sumW(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumE_p(0,1),sumE(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEbis_p(0,1),sumEbis(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEsq_p(0,1),sumEsq(0,1),(nGridT+1)*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_SUM,Master,WHAM_COMM,IERROR)
+ call MPI_Reduce(sumQ_p(1,0,1),sumQ(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Reduce(sumQsq_p(1,0,1),sumQsq(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ call MPI_Reduce(sumEQ_p(1,0,1),sumEQ(1,0,1),
+ & MaxQ1*(nGridT+1)*nParmSet,MPI_DOUBLE_PRECISION,MPI_SUM,Master,
+ & WHAM_COMM,IERROR)
+ if (me.eq.master) then
+#endif
+ write (iout,'(/a)') 'Thermal characteristics of folding'
+ if (nslice.eq.1) then
+ nazwa=prefix
+ else
+ nazwa=prefix(:ilen(prefix))//"_slice_"//licz2
+ endif
+ iln=ilen(nazwa)
+ if (nparmset.eq.1 .and. .not.separate_parset) then
+ nazwa=nazwa(:iln)//".thermal"
+ else if (nparmset.eq.1 .and. separate_parset) then
+ write(licz3,"(bz,i3.3)") myparm
+ nazwa=nazwa(:iln)//"_par_"//licz3//".thermal"
+ endif
+ do iparm=1,nParmSet
+ if (nparmset.gt.1) then
+ write(licz3,"(bz,i3.3)") iparm
+ nazwa=nazwa(:iln)//"_par_"//licz3//".thermal"
+ endif
+ open(34,file=nazwa)
+ if (separate_parset) then
+ write (iout,'(a,i3)') "Parameter set",myparm
+ else
+ write (iout,'(a,i3)') "Parameter set",iparm
+ endif
+ do i=0,NGridT
+ sumE(i,iparm)=sumE(i,iparm)/sumW(i,iparm)
+ sumEbis(i,iparm)=(startGridT+i*delta_T)*sumEbis(i,iparm)/
+ & sumW(i,iparm)
+ sumEsq(i,iparm)=(sumEsq(i,iparm)/sumW(i,iparm)
+ & -sumE(i,iparm)**2)/(1.987D-3*(startGridT+i*delta_T)**2)
+ do j=1,nQ+2
+ sumQ(j,i,iparm)=sumQ(j,i,iparm)/sumW(i,iparm)
+ sumQsq(j,i,iparm)=sumQsq(j,i,iparm)/sumW(i,iparm)
+ & -sumQ(j,i,iparm)**2
+ sumEQ(j,i,iparm)=sumEQ(j,i,iparm)/sumW(i,iparm)
+ & -sumQ(j,i,iparm)*sumE(i,iparm)
+ enddo
+ sumW(i,iparm)=-dlog(sumW(i,iparm))*(1.987D-3*
+ & (startGridT+i*delta_T))+potEmin
+ write (iout,'(f7.1,2f15.5,$)') startGridT+i*delta_T,
+ & sumW(i,iparm),sumE(i,iparm)
+ write (iout,'(f10.5,$)') (sumQ(j,i,iparm),j=1,nQ+2)
+ write (iout,'(e15.5,$)') sumEsq(i,iparm)-sumEbis(i,iparm),
+ & (sumQsq(j,i,iparm),j=1,nQ+2),(sumEQ(j,i,iparm),j=1,nQ+2)
+ write (iout,*)
+ write (34,'(f7.1,2f15.5,$)') startGridT+i*delta_T,
+ & sumW(i,iparm),sumE(i,iparm)
+ write (34,'(f10.5,$)') (sumQ(j,i,iparm),j=1,nQ+2)
+ write (34,'(e15.5,$)') sumEsq(i,iparm)-sumEbis(i,iparm),
+ & (sumQsq(j,i,iparm),j=1,nQ+2),(sumEQ(j,i,iparm),j=1,nQ+2)
+ write (34,*)
+ enddo
+ close(34)
+ enddo
+ if (histout) then
+ do t=0,tmax
+ if (hfin_ent(t).gt.0.0d0) then
+ liczba=t
+ jj = mod(liczba,nbin1)
+ write (iout,'(f6.3,e20.10," ent")') dmin+(jj+0.5d0)*delta,
+ & hfin_ent(t)
+ if (histfile) write (ihist,'(f6.3,e20.10," ent")')
+ & dmin+(jj+0.5d0)*delta,
+ & hfin_ent(t)
+ endif
+ enddo
+ if (histfile) close(ihist)
+ endif
+
+#ifdef ZSCORE
+! Write data for zscore
+ if (nslice.eq.1) then
+ zscname=prefix(:ilen(prefix))//".zsc"
+ else
+ zscname=prefix(:ilen(prefix))//"_slice_"//licz2//".zsc"
+ endif
+#if defined(AIX) || defined(PGI)
+ open (izsc,file=prefix(:ilen(prefix))//'.zsc',position='append')
+#else
+ open (izsc,file=prefix(:ilen(prefix))//'.zsc',access='append')
+#endif
+ write (izsc,'("NQ=",i1," NPARM=",i1)') nQ,nParmSet
+ do iparm=1,nParmSet
+ write (izsc,'("NT=",i1)') nT_h(iparm)
+ do ib=1,nT_h(iparm)
+ write (izsc,'("TEMP=",f6.1," NR=",i2," SNK=",$)')
+ & 1.0d0/(beta_h(ib,iparm)*1.987D-3),nR(ib,iparm)
+ jj = min0(nR(ib,iparm),7)
+ write (izsc,'(i8,$)') (snk(i,ib,iparm,islice),i=1,jj)
+ write (izsc,'(a1,$)') (" ",i=22+8*jj+1,79)
+ write (izsc,'("&")')
+ if (nR(ib,iparm).gt.7) then
+ do ii=8,nR(ib,iparm),9
+ jj = min0(nR(ib,iparm),ii+8)
+ write (izsc,'(i8,$)') (snk(i,ib,iparm,islice),i=ii,jj)
+ write (izsc,'(a1,$') (" ",i=(jj-ii+1)*8+1,79)
+ write (izsc,'("&")')
+ enddo
+ endif
+ write (izsc,'("FI=",$)')
+ jj=min0(nR(ib,iparm),7)
+ write (izsc,'(f10.5,$)') (fi(i,ib,iparm),i=1,jj)
+ write (izsc,'(a1,$)') (" ",i=3+10*jj+1,79)
+ write (izsc,'("&")')
+ if (nR(ib,iparm).gt.7) then
+ do ii=8,nR(ib,iparm),9
+ jj = min0(nR(ib,iparm),ii+8)
+ write (izsc,'(f10.5,$)') (fi(i,ib,iparm),i=ii,jj)
+ if (jj.eq.nR(ib,iparm)) then
+ write (izsc,*)
+ else
+ write (izsc,'(a1,$)') (" ",i=10*(jj-ii+1)+1,79)
+ write (izsc,'(t80,"&")')
+ endif
+ enddo
+ endif
+ do i=1,nR(ib,iparm)
+ write (izsc,'("KH=",$)')
+ write (izsc,'(f7.2,$)') (Kh(j,i,ib,iparm),j=1,nQ)
+ write (izsc,'(" Q0=",$)')
+ write (izsc,'(f7.5,$)') (q0(j,i,ib,iparm),j=1,nQ)
+ write (izsc,*)
+ enddo
+ enddo
+ enddo
+ close(izsc)
+#endif
+#ifdef MPI
+ endif
+#endif
+
+ return
+
+ end
--- /dev/null
+ program WHAM_multparm
+c Creation/update of the database of conformations
+ implicit none
+#ifndef ISNAN
+ external proc_proc
+#endif
+#ifdef WINPGI
+cMS$ATTRIBUTES C :: proc_proc
+#endif
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE
+ include "COMMON.MPI"
+#endif
+ include "COMMON.IOUNITS"
+ include "COMMON.FREE"
+ include "COMMON.CONTROL"
+ include "COMMON.ALLPARM"
+ include "COMMON.PROT"
+ double precision rr,x(max_paropt)
+ integer idumm
+ integer i,ipar,islice
+#ifdef MPI
+ call MPI_Init( IERROR )
+ call MPI_Comm_rank( MPI_COMM_WORLD, me, IERROR )
+ call MPI_Comm_size( MPI_COMM_WORLD, nprocs, IERROR )
+ Master = 0
+ if (ierror.gt.0) then
+ write(iout,*) "SEVERE ERROR - Can't initialize MPI."
+ call mpi_finalize(ierror)
+ stop
+ endif
+ if (nprocs.gt.MaxProcs+1) then
+ write (2,*) "Error - too many processors",
+ & nprocs,MaxProcs+1
+ write (2,*) "Increase MaxProcs and recompile"
+ call MPI_Finalize(IERROR)
+ stop
+ endif
+#endif
+c NaNQ initialization
+#ifndef ISNAN
+ i=-1
+ rr=dacos(100.0d0)
+#ifdef WINPGI
+ idumm=proc_proc(rr,i)
+#else
+ call proc_proc(rr,i)
+#endif
+#endif
+ call initialize
+ call openunits
+ call cinfo
+ call read_general_data(*10)
+ call flush(iout)
+ call molread(*10)
+ call flush(iout)
+#ifdef MPI
+ write (iout,*) "Calling proc_groups"
+ call proc_groups
+ write (iout,*) "proc_groups exited"
+ call flush(iout)
+#endif
+#ifdef SCALREP
+ write (iout,*) "1,4 SCSC repulsive interactions sacled down by 10"
+#endif
+ do ipar=1,nParmSet
+ write (iout,*) "Calling parmread",ipar
+ call parmread(ipar,*10)
+ if (.not.separate_parset) then
+ call store_parm(ipar)
+ write (iout,*) "Finished storing parameters",ipar
+ else if (ipar.eq.myparm) then
+ call store_parm(1)
+ write (iout,*) "Finished storing parameters",ipar
+ endif
+ call flush(iout)
+ enddo
+ call read_efree(*10)
+ write (iout,*) "Finished READ_EFREE"
+ call flush(iout)
+ call read_protein_data(*10)
+ write (iout,*) "Finished READ_PROTEIN_DATA"
+ call flush(iout)
+ if (indpdb.gt.0) then
+ call promienie
+ call read_compar
+ call read_ref_structure(*10)
+ call proc_cont
+ call fragment_list
+ endif
+ write (iout,*) "Begin read_database"
+ call flush(iout)
+ call read_database(*10)
+ write (iout,*) "Finished read_database"
+ call flush(iout)
+ if (separate_parset) nparmset=1
+ do islice=1,nslice
+ if (ntot(islice).gt.0) then
+#ifdef MPI
+ call work_partition(islice,.true.)
+ write (iout,*) "work_partition OK"
+ call flush(iout)
+#endif
+ call enecalc(islice,*10)
+ write (iout,*) "enecalc OK"
+ call flush(iout)
+ write (iout,*) "Calling WHAM_calc"
+ call flush(iout)
+ call WHAM_CALC(islice,*10)
+ write (iout,*) "wham_calc OK"
+ call flush(iout)
+ call write_dbase(islice,*10)
+ write (iout,*) "write_dbase OK"
+ call flush(iout)
+ if (ensembles.gt.0) then
+ call make_ensembles(islice,*10)
+ write (iout,*) "make_ensembles OK"
+ call flush(iout)
+ endif
+ endif
+ enddo
+#ifdef MPI
+ call MPI_Finalize( IERROR )
+#endif
+ stop
+ 10 write (iout,*) "Error termination of the program"
+ call MPI_Finalize( IERROR )
+ stop
+ end
+c------------------------------------------------------------------------------
+#ifdef MPI
+ subroutine proc_groups
+C Split the processors into the Master and Workers group, if needed.
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "mpif.h"
+ include "COMMON.IOUNITS"
+ include "COMMON.MPI"
+ include "COMMON.FREE"
+ integer n,chunk,i,j,ii,remainder
+ integer kolor,key,ierror,errcode
+ logical lprint
+ lprint=.true.
+C
+C Split the communicator if independent runs for different parameter
+C sets will be performed.
+C
+ if (nparmset.eq.1 .or. .not.separate_parset) then
+ WHAM_COMM = MPI_COMM_WORLD
+ else if (separate_parset) then
+ if (nprocs.lt.nparmset) then
+ write (iout,*)
+ & "*** Cannot split parameter sets for fewer processors than sets",
+ & nprocs,nparmset
+ call MPI_Finalize(ierror)
+ stop
+ endif
+ write (iout,*) "nparmset",nparmset
+ nprocs = nprocs/nparmset
+ kolor = me/nprocs
+ key = mod(me,nprocs)
+ write (iout,*) "My old rank",me," kolor",kolor," key",key
+ call MPI_Comm_split(MPI_COMM_WORLD,kolor,key,WHAM_COMM,ierror)
+ call MPI_Comm_size(WHAM_COMM,nprocs,ierror)
+ call MPI_Comm_rank(WHAM_COMM,me,ierror)
+ write (iout,*) "My new rank",me," comm size",nprocs
+ write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
+ & " WHAM_COMM",WHAM_COMM
+ myparm=kolor+1
+ write (iout,*) "My parameter set is",myparm
+ call flush(iout)
+ else
+ myparm=nparmset
+ endif
+ Me1 = Me
+ Nprocs1 = Nprocs
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine work_partition(islice,lprint)
+c Split the conformations between processors
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ include "mpif.h"
+ include "COMMON.IOUNITS"
+ include "COMMON.MPI"
+ include "COMMON.PROT"
+ integer islice
+ integer n,chunk,i,j,ii,remainder
+ integer kolor,key,ierror,errcode
+ logical lprint
+C
+C Divide conformations between processors; the first and
+C the last conformation to handle by ith processor is stored in
+C indstart(i) and indend(i), respectively.
+C
+C First try to assign equal number of conformations to each processor.
+C
+ n=ntot(islice)
+ write (iout,*) "n=",n
+ indstart(0)=1
+ chunk = N/nprocs1
+ scount(0) = chunk
+c print *,"i",0," indstart",indstart(0)," scount",
+c & scount(0)
+ do i=1,nprocs1-1
+ indstart(i)=chunk+indstart(i-1)
+ scount(i)=scount(i-1)
+c print *,"i",i," indstart",indstart(i)," scount",
+c & scount(i)
+ enddo
+C
+C Determine how many conformations remained yet unassigned.
+C
+ remainder=N-(indstart(nprocs1-1)
+ & +scount(nprocs1-1)-1)
+c print *,"remainder",remainder
+C
+C Assign the remainder conformations to consecutive processors, starting
+C from the lowest rank; this continues until the list is exhausted.
+C
+ if (remainder .gt. 0) then
+ do i=1,remainder
+ scount(i-1) = scount(i-1) + 1
+ indstart(i) = indstart(i) + i
+ enddo
+ do i=remainder+1,nprocs1-1
+ indstart(i) = indstart(i) + remainder
+ enddo
+ endif
+
+ indstart(nprocs1)=N+1
+ scount(nprocs1)=0
+
+ do i=0,NProcs1
+ indend(i)=indstart(i)+scount(i)-1
+ idispl(i)=indstart(i)-1
+ enddo
+
+ N=0
+ do i=0,Nprocs1-1
+ N=N+indend(i)-indstart(i)+1
+ enddo
+
+c print *,"N",n," NTOT",ntot(islice)
+ if (N.ne.ntot(islice)) then
+ write (iout,*) "!!! Checksum error on processor",me,
+ & " slice",islice
+ call flush(iout)
+ call MPI_Abort( MPI_COMM_WORLD, Ierror, Errcode )
+ endif
+
+ if (lprint) then
+ write (iout,*) "Partition of work between processors"
+ do i=0,nprocs1-1
+ write (iout,'(a,i5,a,i7,a,i7,a,i7)')
+ & "Processor",i," indstart",indstart(i),
+ & " indend",indend(i)," count",scount(i)
+ enddo
+ endif
+ return
+ end
+#endif
+#ifdef AIX
+ subroutine flush(iu)
+ call flush_(iu)
+ return
+ end
+#endif
--- /dev/null
+# This make file is part of the xdrf package.
+#
+# (C) 1995 Frans van Hoesel, hoesel@chem.rug.nl
+#
+# 2006 modified by Cezary Czaplewski
+
+# Set C compiler and flags for ARCH
+CC = cc
+CFLAGS = -O
+
+M4 = m4
+M4FILE = underscore.m4
+
+libxdrf.a: libxdrf.o ftocstr.o
+ ar cr libxdrf.a $?
+
+clean:
+ rm -f libxdrf.o ftocstr.o libxdrf.a
+
+ftocstr.o: ftocstr.c
+ $(CC) $(CFLAGS) -c ftocstr.c
+
+libxdrf.o: libxdrf.m4 $(M4FILE)
+ $(M4) $(M4FILE) libxdrf.m4 > libxdrf.c
+ $(CC) $(CFLAGS) -c libxdrf.c
+ rm -f libxdrf.c
+
--- /dev/null
+
+
+int ftocstr(ds, dl, ss, sl)
+ char *ds, *ss; /* dst, src ptrs */
+ int dl; /* dst max len */
+ int sl; /* src len */
+{
+ char *p;
+
+ for (p = ss + sl; --p >= ss && *p == ' '; ) ;
+ sl = p - ss + 1;
+ dl--;
+ ds[0] = 0;
+ if (sl > dl)
+ return 1;
+ while (sl--)
+ (*ds++ = *ss++);
+ *ds = '\0';
+ return 0;
+}
+
+
+int ctofstr(ds, dl, ss)
+ char *ds; /* dest space */
+ int dl; /* max dest length */
+ char *ss; /* src string (0-term) */
+{
+ while (dl && *ss) {
+ *ds++ = *ss++;
+ dl--;
+ }
+ while (dl--)
+ *ds++ = ' ';
+ return 0;
+}
--- /dev/null
+/*____________________________________________________________________________
+ |
+ | libxdrf - portable fortran interface to xdr. some xdr routines
+ | are C routines for compressed coordinates
+ |
+ | version 1.1
+ |
+ | This collection of routines is intended to write and read
+ | data in a portable way to a file, so data written on one type
+ | of machine can be read back on a different type.
+ |
+ | all fortran routines use an integer 'xdrid', which is an id to the
+ | current xdr file, and is set by xdrfopen.
+ | most routines have in integer 'ret' which is the return value.
+ | The value of 'ret' is zero on failure, and most of the time one
+ | on succes.
+ |
+ | There are three routines useful for C users:
+ | xdropen(), xdrclose(), xdr3dfcoord().
+ | The first two replace xdrstdio_create and xdr_destroy, and *must* be
+ | used when you plan to use xdr3dfcoord(). (they are also a bit
+ | easier to interface). For writing data other than compressed coordinates
+ | you should use the standard C xdr routines (see xdr man page)
+ |
+ | xdrfopen(xdrid, filename, mode, ret)
+ | character *(*) filename
+ | character *(*) mode
+ |
+ | this will open the file with the given filename (string)
+ | and the given mode, it returns an id in xdrid, which is
+ | to be used in all other calls to xdrf routines.
+ | mode is 'w' to create, or update an file, for all other
+ | values of mode the file is opened for reading
+ |
+ | you need to call xdrfclose to flush the output and close
+ | the file.
+ | Note that you should not use xdrstdio_create, which comes with the
+ | standard xdr library
+ |
+ | xdrfclose(xdrid, ret)
+ | flush the data to the file, and closes the file;
+ | You should not use xdr_destroy (which comes standard with
+ | the xdr libraries.
+ |
+ | xdrfbool(xdrid, bp, ret)
+ | integer pb
+ |
+ | This filter produces values of either 1 or 0
+ |
+ | xdrfchar(xdrid, cp, ret)
+ | character cp
+ |
+ | filter that translate between characters and their xdr representation
+ | Note that the characters in not compressed and occupies 4 bytes.
+ |
+ | xdrfdouble(xdrid, dp, ret)
+ | double dp
+ |
+ | read/write a double.
+ |
+ | xdrffloat(xdrid, fp, ret)
+ | float fp
+ |
+ | read/write a float.
+ |
+ | xdrfint(xdrid, ip, ret)
+ | integer ip
+ |
+ | read/write integer.
+ |
+ | xdrflong(xdrid, lp, ret)
+ | integer lp
+ |
+ | this routine has a possible portablility problem due to 64 bits longs.
+ |
+ | xdrfshort(xdrid, sp, ret)
+ | integer *2 sp
+ |
+ | xdrfstring(xdrid, sp, maxsize, ret)
+ | character *(*)
+ | integer maxsize
+ |
+ | read/write a string, with maximum length given by maxsize
+ |
+ | xdrfwrapstring(xdris, sp, ret)
+ | character *(*)
+ |
+ | read/write a string (it is the same as xdrfstring accept that it finds
+ | the stringlength itself.
+ |
+ | xdrfvector(xdrid, cp, size, xdrfproc, ret)
+ | character *(*)
+ | integer size
+ | external xdrfproc
+ |
+ | read/write an array pointed to by cp, with number of elements
+ | defined by 'size'. the routine 'xdrfproc' is the name
+ | of one of the above routines to read/write data (like xdrfdouble)
+ | In contrast with the c-version you don't need to specify the
+ | byte size of an element.
+ | xdrfstring is not allowed here (it is in the c version)
+ |
+ | xdrf3dfcoord(xdrid, fp, size, precision, ret)
+ | real (*) fp
+ | real precision
+ | integer size
+ |
+ | this is *NOT* a standard xdr routine. I named it this way, because
+ | it invites people to use the other xdr routines.
+ | It is introduced to store specifically 3d coordinates of molecules
+ | (as found in molecular dynamics) and it writes it in a compressed way.
+ | It starts by multiplying all numbers by precision and
+ | rounding the result to integer. effectively converting
+ | all floating point numbers to fixed point.
+ | it uses an algorithm for compression that is optimized for
+ | molecular data, but could be used for other 3d coordinates
+ | as well. There is subtantial overhead involved, so call this
+ | routine only if you have a large number of coordinates to read/write
+ |
+ | ________________________________________________________________________
+ |
+ | Below are the routines to be used by C programmers. Use the 'normal'
+ | xdr routines to write integers, floats, etc (see man xdr)
+ |
+ | int xdropen(XDR *xdrs, const char *filename, const char *type)
+ | This will open the file with the given filename and the
+ | given mode. You should pass it an allocated XDR struct
+ | in xdrs, to be used in all other calls to xdr routines.
+ | Mode is 'w' to create, or update an file, and for all
+ | other values of mode the file is opened for reading.
+ | You need to call xdrclose to flush the output and close
+ | the file.
+ |
+ | Note that you should not use xdrstdio_create, which
+ | comes with the standard xdr library.
+ |
+ | int xdrclose(XDR *xdrs)
+ | Flush the data to the file, and close the file;
+ | You should not use xdr_destroy (which comes standard
+ | with the xdr libraries).
+ |
+ | int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
+ | This is \fInot\fR a standard xdr routine. I named it this
+ | way, because it invites people to use the other xdr
+ | routines.
+ |
+ | (c) 1995 Frans van Hoesel, hoesel@chem.rug.nl
+*/
+
+
+#include <limits.h>
+#include <malloc.h>
+#include <math.h>
+#include <rpc/rpc.h>
+#include <rpc/xdr.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "xdrf.h"
+
+int ftocstr(char *, int, char *, int);
+int ctofstr(char *, int, char *);
+
+#define MAXID 20
+static FILE *xdrfiles[MAXID];
+static XDR *xdridptr[MAXID];
+static char xdrmodes[MAXID];
+static unsigned int cnt;
+
+typedef void (* FUNCTION(xdrfproc)) (int *, void *, int *);
+
+void
+FUNCTION(xdrfbool) ARGS(`xdrid, pb, ret')
+int *xdrid, *ret;
+int *pb;
+{
+ *ret = xdr_bool(xdridptr[*xdrid], (bool_t *) pb);
+ cnt += sizeof(int);
+}
+
+void
+FUNCTION(xdrfchar) ARGS(`xdrid, cp, ret')
+int *xdrid, *ret;
+char *cp;
+{
+ *ret = xdr_char(xdridptr[*xdrid], cp);
+ cnt += sizeof(char);
+}
+
+void
+FUNCTION(xdrfdouble) ARGS(`xdrid, dp, ret')
+int *xdrid, *ret;
+double *dp;
+{
+ *ret = xdr_double(xdridptr[*xdrid], dp);
+ cnt += sizeof(double);
+}
+
+void
+FUNCTION(xdrffloat) ARGS(`xdrid, fp, ret')
+int *xdrid, *ret;
+float *fp;
+{
+ *ret = xdr_float(xdridptr[*xdrid], fp);
+ cnt += sizeof(float);
+}
+
+void
+FUNCTION(xdrfint) ARGS(`xdrid, ip, ret')
+int *xdrid, *ret;
+int *ip;
+{
+ *ret = xdr_int(xdridptr[*xdrid], ip);
+ cnt += sizeof(int);
+}
+
+void
+FUNCTION(xdrflong) ARGS(`xdrid, lp, ret')
+int *xdrid, *ret;
+long *lp;
+{
+ *ret = xdr_long(xdridptr[*xdrid], lp);
+ cnt += sizeof(long);
+}
+
+void
+FUNCTION(xdrfshort) ARGS(`xdrid, sp, ret')
+int *xdrid, *ret;
+short *sp;
+{
+ *ret = xdr_short(xdridptr[*xdrid], sp);
+ cnt += sizeof(sp);
+}
+
+void
+FUNCTION(xdrfuchar) ARGS(`xdrid, ucp, ret')
+int *xdrid, *ret;
+char *ucp;
+{
+ *ret = xdr_u_char(xdridptr[*xdrid], ucp);
+ cnt += sizeof(char);
+}
+
+void
+FUNCTION(xdrfulong) ARGS(`xdrid, ulp, ret')
+int *xdrid, *ret;
+unsigned long *ulp;
+{
+ *ret = xdr_u_long(xdridptr[*xdrid], ulp);
+ cnt += sizeof(unsigned long);
+}
+
+void
+FUNCTION(xdrfushort) ARGS(`xdrid, usp, ret')
+int *xdrid, *ret;
+unsigned short *usp;
+{
+ *ret = xdr_u_short(xdridptr[*xdrid], usp);
+ cnt += sizeof(unsigned short);
+}
+
+void
+FUNCTION(xdrf3dfcoord) ARGS(`xdrid, fp, size, precision, ret')
+int *xdrid, *ret;
+float *fp;
+int *size;
+float *precision;
+{
+ *ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
+}
+
+void
+FUNCTION(xdrfstring) ARGS(`xdrid, STRING_ARG(sp), maxsize, ret')
+int *xdrid, *ret;
+STRING_ARG_DECL(sp);
+int *maxsize;
+{
+ char *tsp;
+
+ tsp = (char*) malloc(((STRING_LEN(sp)) + 1) * sizeof(char));
+ if (tsp == NULL) {
+ *ret = -1;
+ return;
+ }
+ if (ftocstr(tsp, *maxsize+1, STRING_PTR(sp), STRING_LEN(sp))) {
+ *ret = -1;
+ free(tsp);
+ return;
+ }
+ *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int) *maxsize);
+ ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
+ cnt += *maxsize;
+ free(tsp);
+}
+
+void
+FUNCTION(xdrfwrapstring) ARGS(`xdrid, STRING_ARG(sp), ret')
+int *xdrid, *ret;
+STRING_ARG_DECL(sp);
+{
+ char *tsp;
+ int maxsize;
+ maxsize = (STRING_LEN(sp)) + 1;
+ tsp = (char*) malloc(maxsize * sizeof(char));
+ if (tsp == NULL) {
+ *ret = -1;
+ return;
+ }
+ if (ftocstr(tsp, maxsize, STRING_PTR(sp), STRING_LEN(sp))) {
+ *ret = -1;
+ free(tsp);
+ return;
+ }
+ *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int)maxsize);
+ ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
+ cnt += maxsize;
+ free(tsp);
+}
+
+void
+FUNCTION(xdrfopaque) ARGS(`xdrid, cp, ccnt, ret')
+int *xdrid, *ret;
+caddr_t *cp;
+int *ccnt;
+{
+ *ret = xdr_opaque(xdridptr[*xdrid], (caddr_t)*cp, (u_int)*ccnt);
+ cnt += *ccnt;
+}
+
+void
+FUNCTION(xdrfsetpos) ARGS(`xdrid, pos, ret')
+int *xdrid, *ret;
+int *pos;
+{
+ *ret = xdr_setpos(xdridptr[*xdrid], (u_int) *pos);
+}
+
+void
+FUNCTION(xdrf) ARGS(`xdrid, pos')
+int *xdrid, *pos;
+{
+ *pos = xdr_getpos(xdridptr[*xdrid]);
+}
+
+void
+FUNCTION(xdrfvector) ARGS(`xdrid, cp, size, elproc, ret')
+int *xdrid, *ret;
+char *cp;
+int *size;
+FUNCTION(xdrfproc) elproc;
+{
+ int lcnt;
+ cnt = 0;
+ for (lcnt = 0; lcnt < *size; lcnt++) {
+ elproc(xdrid, (cp+cnt) , ret);
+ }
+}
+
+
+void
+FUNCTION(xdrfclose) ARGS(`xdrid, ret')
+int *xdrid;
+int *ret;
+{
+ *ret = xdrclose(xdridptr[*xdrid]);
+ cnt = 0;
+}
+
+void
+FUNCTION(xdrfopen) ARGS(`xdrid, STRING_ARG(fp), STRING_ARG(mode), ret')
+int *xdrid;
+STRING_ARG_DECL(fp);
+STRING_ARG_DECL(mode);
+int *ret;
+{
+ char fname[512];
+ char fmode[3];
+
+ if (ftocstr(fname, sizeof(fname), STRING_PTR(fp), STRING_LEN(fp))) {
+ *ret = 0;
+ }
+ if (ftocstr(fmode, sizeof(fmode), STRING_PTR(mode),
+ STRING_LEN(mode))) {
+ *ret = 0;
+ }
+
+ *xdrid = xdropen(NULL, fname, fmode);
+ if (*xdrid == 0)
+ *ret = 0;
+ else
+ *ret = 1;
+}
+
+/*___________________________________________________________________________
+ |
+ | what follows are the C routines for opening, closing xdr streams
+ | and the routine to read/write compressed coordinates together
+ | with some routines to assist in this task (those are marked
+ | static and cannot be called from user programs)
+*/
+#define MAXABS INT_MAX-2
+
+#ifndef MIN
+#define MIN(x,y) ((x) < (y) ? (x):(y))
+#endif
+#ifndef MAX
+#define MAX(x,y) ((x) > (y) ? (x):(y))
+#endif
+#ifndef SQR
+#define SQR(x) ((x)*(x))
+#endif
+static int magicints[] = {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
+ 80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
+ 812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
+ 8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
+ 82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
+ 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304, 5284491, 6658042,
+ 8388607, 10568983, 13316085, 16777216 };
+
+#define FIRSTIDX 9
+/* note that magicints[FIRSTIDX-1] == 0 */
+#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
+
+
+/*__________________________________________________________________________
+ |
+ | xdropen - open xdr file
+ |
+ | This versions differs from xdrstdio_create, because I need to know
+ | the state of the file (read or write) so I can use xdr3dfcoord
+ | in eigther read or write mode, and the file descriptor
+ | so I can close the file (something xdr_destroy doesn't do).
+ |
+*/
+
+int xdropen(XDR *xdrs, const char *filename, const char *type) {
+ static int init_done = 0;
+ enum xdr_op lmode;
+ const char *type1;
+ int xdrid;
+
+ if (init_done == 0) {
+ for (xdrid = 1; xdrid < MAXID; xdrid++) {
+ xdridptr[xdrid] = NULL;
+ }
+ init_done = 1;
+ }
+ xdrid = 1;
+ while (xdrid < MAXID && xdridptr[xdrid] != NULL) {
+ xdrid++;
+ }
+ if (xdrid == MAXID) {
+ return 0;
+ }
+ if (*type == 'w' || *type == 'W') {
+ type = "w+";
+ type1 = "a+";
+ lmode = XDR_ENCODE;
+ } else {
+ type = "r";
+ type1 = "r";
+ lmode = XDR_DECODE;
+ }
+ xdrfiles[xdrid] = fopen(filename, type1);
+ if (xdrfiles[xdrid] == NULL) {
+ xdrs = NULL;
+ return 0;
+ }
+ xdrmodes[xdrid] = *type;
+ /* next test isn't usefull in the case of C language
+ * but is used for the Fortran interface
+ * (C users are expected to pass the address of an already allocated
+ * XDR staructure)
+ */
+ if (xdrs == NULL) {
+ xdridptr[xdrid] = (XDR *) malloc(sizeof(XDR));
+ xdrstdio_create(xdridptr[xdrid], xdrfiles[xdrid], lmode);
+ } else {
+ xdridptr[xdrid] = xdrs;
+ xdrstdio_create(xdrs, xdrfiles[xdrid], lmode);
+ }
+ return xdrid;
+}
+
+/*_________________________________________________________________________
+ |
+ | xdrclose - close a xdr file
+ |
+ | This will flush the xdr buffers, and destroy the xdr stream.
+ | It also closes the associated file descriptor (this is *not*
+ | done by xdr_destroy).
+ |
+*/
+
+int xdrclose(XDR *xdrs) {
+ int xdrid;
+
+ if (xdrs == NULL) {
+ fprintf(stderr, "xdrclose: passed a NULL pointer\n");
+ exit(1);
+ }
+ for (xdrid = 1; xdrid < MAXID; xdrid++) {
+ if (xdridptr[xdrid] == xdrs) {
+
+ xdr_destroy(xdrs);
+ fclose(xdrfiles[xdrid]);
+ xdridptr[xdrid] = NULL;
+ return 1;
+ }
+ }
+ fprintf(stderr, "xdrclose: no such open xdr file\n");
+ exit(1);
+
+}
+
+/*____________________________________________________________________________
+ |
+ | sendbits - encode num into buf using the specified number of bits
+ |
+ | This routines appends the value of num to the bits already present in
+ | the array buf. You need to give it the number of bits to use and you
+ | better make sure that this number of bits is enough to hold the value
+ | Also num must be positive.
+ |
+*/
+
+static void sendbits(int buf[], int num_of_bits, int num) {
+
+ unsigned int cnt, lastbyte;
+ int lastbits;
+ unsigned char * cbuf;
+
+ cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
+ cnt = (unsigned int) buf[0];
+ lastbits = buf[1];
+ lastbyte =(unsigned int) buf[2];
+ while (num_of_bits >= 8) {
+ lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
+ cbuf[cnt++] = lastbyte >> lastbits;
+ num_of_bits -= 8;
+ }
+ if (num_of_bits > 0) {
+ lastbyte = (lastbyte << num_of_bits) | num;
+ lastbits += num_of_bits;
+ if (lastbits >= 8) {
+ lastbits -= 8;
+ cbuf[cnt++] = lastbyte >> lastbits;
+ }
+ }
+ buf[0] = cnt;
+ buf[1] = lastbits;
+ buf[2] = lastbyte;
+ if (lastbits>0) {
+ cbuf[cnt] = lastbyte << (8 - lastbits);
+ }
+}
+
+/*_________________________________________________________________________
+ |
+ | sizeofint - calculate bitsize of an integer
+ |
+ | return the number of bits needed to store an integer with given max size
+ |
+*/
+
+static int sizeofint(const int size) {
+ unsigned int num = 1;
+ int num_of_bits = 0;
+
+ while (size >= num && num_of_bits < 32) {
+ num_of_bits++;
+ num <<= 1;
+ }
+ return num_of_bits;
+}
+
+/*___________________________________________________________________________
+ |
+ | sizeofints - calculate 'bitsize' of compressed ints
+ |
+ | given the number of small unsigned integers and the maximum value
+ | return the number of bits needed to read or write them with the
+ | routines receiveints and sendints. You need this parameter when
+ | calling these routines. Note that for many calls I can use
+ | the variable 'smallidx' which is exactly the number of bits, and
+ | So I don't need to call 'sizeofints for those calls.
+*/
+
+static int sizeofints( const int num_of_ints, unsigned int sizes[]) {
+ int i, num;
+ unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
+ num_of_bytes = 1;
+ bytes[0] = 1;
+ num_of_bits = 0;
+ for (i=0; i < num_of_ints; i++) {
+ tmp = 0;
+ for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
+ tmp = bytes[bytecnt] * sizes[i] + tmp;
+ bytes[bytecnt] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ while (tmp != 0) {
+ bytes[bytecnt++] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ num_of_bytes = bytecnt;
+ }
+ num = 1;
+ num_of_bytes--;
+ while (bytes[num_of_bytes] >= num) {
+ num_of_bits++;
+ num *= 2;
+ }
+ return num_of_bits + num_of_bytes * 8;
+
+}
+
+/*____________________________________________________________________________
+ |
+ | sendints - send a small set of small integers in compressed format
+ |
+ | this routine is used internally by xdr3dfcoord, to send a set of
+ | small integers to the buffer.
+ | Multiplication with fixed (specified maximum ) sizes is used to get
+ | to one big, multibyte integer. Allthough the routine could be
+ | modified to handle sizes bigger than 16777216, or more than just
+ | a few integers, this is not done, because the gain in compression
+ | isn't worth the effort. Note that overflowing the multiplication
+ | or the byte buffer (32 bytes) is unchecked and causes bad results.
+ |
+ */
+
+static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
+ unsigned int sizes[], unsigned int nums[]) {
+
+ int i;
+ unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
+
+ tmp = nums[0];
+ num_of_bytes = 0;
+ do {
+ bytes[num_of_bytes++] = tmp & 0xff;
+ tmp >>= 8;
+ } while (tmp != 0);
+
+ for (i = 1; i < num_of_ints; i++) {
+ if (nums[i] >= sizes[i]) {
+ fprintf(stderr,"major breakdown in sendints num %d doesn't "
+ "match size %d\n", nums[i], sizes[i]);
+ exit(1);
+ }
+ /* use one step multiply */
+ tmp = nums[i];
+ for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
+ tmp = bytes[bytecnt] * sizes[i] + tmp;
+ bytes[bytecnt] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ while (tmp != 0) {
+ bytes[bytecnt++] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ num_of_bytes = bytecnt;
+ }
+ if (num_of_bits >= num_of_bytes * 8) {
+ for (i = 0; i < num_of_bytes; i++) {
+ sendbits(buf, 8, bytes[i]);
+ }
+ sendbits(buf, num_of_bits - num_of_bytes * 8, 0);
+ } else {
+ for (i = 0; i < num_of_bytes-1; i++) {
+ sendbits(buf, 8, bytes[i]);
+ }
+ sendbits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
+ }
+}
+
+
+/*___________________________________________________________________________
+ |
+ | receivebits - decode number from buf using specified number of bits
+ |
+ | extract the number of bits from the array buf and construct an integer
+ | from it. Return that value.
+ |
+*/
+
+static int receivebits(int buf[], int num_of_bits) {
+
+ int cnt, num;
+ unsigned int lastbits, lastbyte;
+ unsigned char * cbuf;
+ int mask = (1 << num_of_bits) -1;
+
+ cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
+ cnt = buf[0];
+ lastbits = (unsigned int) buf[1];
+ lastbyte = (unsigned int) buf[2];
+
+ num = 0;
+ while (num_of_bits >= 8) {
+ lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
+ num |= (lastbyte >> lastbits) << (num_of_bits - 8);
+ num_of_bits -=8;
+ }
+ if (num_of_bits > 0) {
+ if (lastbits < num_of_bits) {
+ lastbits += 8;
+ lastbyte = (lastbyte << 8) | cbuf[cnt++];
+ }
+ lastbits -= num_of_bits;
+ num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
+ }
+ num &= mask;
+ buf[0] = cnt;
+ buf[1] = lastbits;
+ buf[2] = lastbyte;
+ return num;
+}
+
+/*____________________________________________________________________________
+ |
+ | receiveints - decode 'small' integers from the buf array
+ |
+ | this routine is the inverse from sendints() and decodes the small integers
+ | written to buf by calculating the remainder and doing divisions with
+ | the given sizes[]. You need to specify the total number of bits to be
+ | used from buf in num_of_bits.
+ |
+*/
+
+static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
+ unsigned int sizes[], int nums[]) {
+ int bytes[32];
+ int i, j, num_of_bytes, p, num;
+
+ bytes[1] = bytes[2] = bytes[3] = 0;
+ num_of_bytes = 0;
+ while (num_of_bits > 8) {
+ bytes[num_of_bytes++] = receivebits(buf, 8);
+ num_of_bits -= 8;
+ }
+ if (num_of_bits > 0) {
+ bytes[num_of_bytes++] = receivebits(buf, num_of_bits);
+ }
+ for (i = num_of_ints-1; i > 0; i--) {
+ num = 0;
+ for (j = num_of_bytes-1; j >=0; j--) {
+ num = (num << 8) | bytes[j];
+ p = num / sizes[i];
+ bytes[j] = p;
+ num = num - p * sizes[i];
+ }
+ nums[i] = num;
+ }
+ nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
+}
+
+/*____________________________________________________________________________
+ |
+ | xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
+ |
+ | this routine reads or writes (depending on how you opened the file with
+ | xdropen() ) a large number of 3d coordinates (stored in *fp).
+ | The number of coordinates triplets to write is given by *size. On
+ | read this number may be zero, in which case it reads as many as were written
+ | or it may specify the number if triplets to read (which should match the
+ | number written).
+ | Compression is achieved by first converting all floating numbers to integer
+ | using multiplication by *precision and rounding to the nearest integer.
+ | Then the minimum and maximum value are calculated to determine the range.
+ | The limited range of integers so found, is used to compress the coordinates.
+ | In addition the differences between succesive coordinates is calculated.
+ | If the difference happens to be 'small' then only the difference is saved,
+ | compressing the data even more. The notion of 'small' is changed dynamically
+ | and is enlarged or reduced whenever needed or possible.
+ | Extra compression is achieved in the case of GROMOS and coordinates of
+ | water molecules. GROMOS first writes out the Oxygen position, followed by
+ | the two hydrogens. In order to make the differences smaller (and thereby
+ | compression the data better) the order is changed into first one hydrogen
+ | then the oxygen, followed by the other hydrogen. This is rather special, but
+ | it shouldn't harm in the general case.
+ |
+ */
+
+int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) {
+
+
+ static int *ip = NULL;
+ static int oldsize;
+ static int *buf;
+
+ int minint[3], maxint[3], mindiff, *lip, diff;
+ int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
+ int minidx, maxidx;
+ unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
+ int flag, k;
+ int small, smaller, larger, i, is_small, is_smaller, run, prevrun;
+ float *lfp, lf;
+ int tmp, *thiscoord, prevcoord[3];
+ unsigned int tmpcoord[30];
+
+ int bufsize, xdrid, lsize;
+ unsigned int bitsize;
+ float inv_precision;
+ int errval = 1;
+
+ /* find out if xdrs is opened for reading or for writing */
+ xdrid = 0;
+ while (xdridptr[xdrid] != xdrs) {
+ xdrid++;
+ if (xdrid >= MAXID) {
+ fprintf(stderr, "xdr error. no open xdr stream\n");
+ exit (1);
+ }
+ }
+ if (xdrmodes[xdrid] == 'w') {
+
+ /* xdrs is open for writing */
+
+ if (xdr_int(xdrs, size) == 0)
+ return 0;
+ size3 = *size * 3;
+ /* when the number of coordinates is small, don't try to compress; just
+ * write them as floats using xdr_vector
+ */
+ if (*size <= 9 ) {
+ return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
+ (xdrproc_t)xdr_float));
+ }
+
+ xdr_float(xdrs, precision);
+ if (ip == NULL) {
+ ip = (int *)malloc(size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)malloc(bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ } else if (*size > oldsize) {
+ ip = (int *)realloc(ip, size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)realloc(buf, bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ }
+ /* buf[0-2] are special and do not contain actual data */
+ buf[0] = buf[1] = buf[2] = 0;
+ minint[0] = minint[1] = minint[2] = INT_MAX;
+ maxint[0] = maxint[1] = maxint[2] = INT_MIN;
+ prevrun = -1;
+ lfp = fp;
+ lip = ip;
+ mindiff = INT_MAX;
+ oldlint1 = oldlint2 = oldlint3 = 0;
+ while(lfp < fp + size3 ) {
+ /* find nearest integer */
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint1 = lf;
+ if (lint1 < minint[0]) minint[0] = lint1;
+ if (lint1 > maxint[0]) maxint[0] = lint1;
+ *lip++ = lint1;
+ lfp++;
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint2 = lf;
+ if (lint2 < minint[1]) minint[1] = lint2;
+ if (lint2 > maxint[1]) maxint[1] = lint2;
+ *lip++ = lint2;
+ lfp++;
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint3 = lf;
+ if (lint3 < minint[2]) minint[2] = lint3;
+ if (lint3 > maxint[2]) maxint[2] = lint3;
+ *lip++ = lint3;
+ lfp++;
+ diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
+ if (diff < mindiff && lfp > fp + 3)
+ mindiff = diff;
+ oldlint1 = lint1;
+ oldlint2 = lint2;
+ oldlint3 = lint3;
+ }
+ xdr_int(xdrs, &(minint[0]));
+ xdr_int(xdrs, &(minint[1]));
+ xdr_int(xdrs, &(minint[2]));
+
+ xdr_int(xdrs, &(maxint[0]));
+ xdr_int(xdrs, &(maxint[1]));
+ xdr_int(xdrs, &(maxint[2]));
+
+ if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
+ (float)maxint[1] - (float)minint[1] >= MAXABS ||
+ (float)maxint[2] - (float)minint[2] >= MAXABS) {
+ /* turning value in unsigned by subtracting minint
+ * would cause overflow
+ */
+ errval = 0;
+ }
+ sizeint[0] = maxint[0] - minint[0]+1;
+ sizeint[1] = maxint[1] - minint[1]+1;
+ sizeint[2] = maxint[2] - minint[2]+1;
+
+ /* check if one of the sizes is to big to be multiplied */
+ if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
+ bitsizeint[0] = sizeofint(sizeint[0]);
+ bitsizeint[1] = sizeofint(sizeint[1]);
+ bitsizeint[2] = sizeofint(sizeint[2]);
+ bitsize = 0; /* flag the use of large sizes */
+ } else {
+ bitsize = sizeofints(3, sizeint);
+ }
+ lip = ip;
+ luip = (unsigned int *) ip;
+ smallidx = FIRSTIDX;
+ while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
+ smallidx++;
+ }
+ xdr_int(xdrs, &smallidx);
+ maxidx = MIN(LASTIDX, smallidx + 8) ;
+ minidx = maxidx - 8; /* often this equal smallidx */
+ smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+ small = magicints[smallidx] / 2;
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
+ larger = magicints[maxidx] / 2;
+ i = 0;
+ while (i < *size) {
+ is_small = 0;
+ thiscoord = (int *)(luip) + i * 3;
+ if (smallidx < maxidx && i >= 1 &&
+ abs(thiscoord[0] - prevcoord[0]) < larger &&
+ abs(thiscoord[1] - prevcoord[1]) < larger &&
+ abs(thiscoord[2] - prevcoord[2]) < larger) {
+ is_smaller = 1;
+ } else if (smallidx > minidx) {
+ is_smaller = -1;
+ } else {
+ is_smaller = 0;
+ }
+ if (i + 1 < *size) {
+ if (abs(thiscoord[0] - thiscoord[3]) < small &&
+ abs(thiscoord[1] - thiscoord[4]) < small &&
+ abs(thiscoord[2] - thiscoord[5]) < small) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
+ thiscoord[3] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
+ thiscoord[4] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
+ thiscoord[5] = tmp;
+ is_small = 1;
+ }
+
+ }
+ tmpcoord[0] = thiscoord[0] - minint[0];
+ tmpcoord[1] = thiscoord[1] - minint[1];
+ tmpcoord[2] = thiscoord[2] - minint[2];
+ if (bitsize == 0) {
+ sendbits(buf, bitsizeint[0], tmpcoord[0]);
+ sendbits(buf, bitsizeint[1], tmpcoord[1]);
+ sendbits(buf, bitsizeint[2], tmpcoord[2]);
+ } else {
+ sendints(buf, 3, bitsize, sizeint, tmpcoord);
+ }
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+ thiscoord = thiscoord + 3;
+ i++;
+
+ run = 0;
+ if (is_small == 0 && is_smaller == -1)
+ is_smaller = 0;
+ while (is_small && run < 8*3) {
+ if (is_smaller == -1 && (
+ SQR(thiscoord[0] - prevcoord[0]) +
+ SQR(thiscoord[1] - prevcoord[1]) +
+ SQR(thiscoord[2] - prevcoord[2]) >= smaller * smaller)) {
+ is_smaller = 0;
+ }
+
+ tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small;
+ tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small;
+ tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small;
+
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+
+ i++;
+ thiscoord = thiscoord + 3;
+ is_small = 0;
+ if (i < *size &&
+ abs(thiscoord[0] - prevcoord[0]) < small &&
+ abs(thiscoord[1] - prevcoord[1]) < small &&
+ abs(thiscoord[2] - prevcoord[2]) < small) {
+ is_small = 1;
+ }
+ }
+ if (run != prevrun || is_smaller != 0) {
+ prevrun = run;
+ sendbits(buf, 1, 1); /* flag the change in run-length */
+ sendbits(buf, 5, run+is_smaller+1);
+ } else {
+ sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
+ }
+ for (k=0; k < run; k+=3) {
+ sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
+ }
+ if (is_smaller != 0) {
+ smallidx += is_smaller;
+ if (is_smaller < 0) {
+ small = smaller;
+ smaller = magicints[smallidx-1] / 2;
+ } else {
+ smaller = small;
+ small = magicints[smallidx] / 2;
+ }
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
+ }
+ }
+ if (buf[1] != 0) buf[0]++;;
+ xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
+ return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
+ } else {
+
+ /* xdrs is open for reading */
+
+ if (xdr_int(xdrs, &lsize) == 0)
+ return 0;
+ if (*size != 0 && lsize != *size) {
+ fprintf(stderr, "wrong number of coordinates in xdr3dfcoor; "
+ "%d arg vs %d in file", *size, lsize);
+ }
+ *size = lsize;
+ size3 = *size * 3;
+ if (*size <= 9) {
+ return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
+ (xdrproc_t)xdr_float));
+ }
+ xdr_float(xdrs, precision);
+ if (ip == NULL) {
+ ip = (int *)malloc(size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)malloc(bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ } else if (*size > oldsize) {
+ ip = (int *)realloc(ip, size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)realloc(buf, bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ }
+ buf[0] = buf[1] = buf[2] = 0;
+
+ xdr_int(xdrs, &(minint[0]));
+ xdr_int(xdrs, &(minint[1]));
+ xdr_int(xdrs, &(minint[2]));
+
+ xdr_int(xdrs, &(maxint[0]));
+ xdr_int(xdrs, &(maxint[1]));
+ xdr_int(xdrs, &(maxint[2]));
+
+ sizeint[0] = maxint[0] - minint[0]+1;
+ sizeint[1] = maxint[1] - minint[1]+1;
+ sizeint[2] = maxint[2] - minint[2]+1;
+
+ /* check if one of the sizes is to big to be multiplied */
+ if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
+ bitsizeint[0] = sizeofint(sizeint[0]);
+ bitsizeint[1] = sizeofint(sizeint[1]);
+ bitsizeint[2] = sizeofint(sizeint[2]);
+ bitsize = 0; /* flag the use of large sizes */
+ } else {
+ bitsize = sizeofints(3, sizeint);
+ }
+
+ xdr_int(xdrs, &smallidx);
+ maxidx = MIN(LASTIDX, smallidx + 8) ;
+ minidx = maxidx - 8; /* often this equal smallidx */
+ smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+ small = magicints[smallidx] / 2;
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
+ larger = magicints[maxidx];
+
+ /* buf[0] holds the length in bytes */
+
+ if (xdr_int(xdrs, &(buf[0])) == 0)
+ return 0;
+ if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
+ return 0;
+ buf[0] = buf[1] = buf[2] = 0;
+
+ lfp = fp;
+ inv_precision = 1.0 / * precision;
+ run = 0;
+ i = 0;
+ lip = ip;
+ while ( i < lsize ) {
+ thiscoord = (int *)(lip) + i * 3;
+
+ if (bitsize == 0) {
+ thiscoord[0] = receivebits(buf, bitsizeint[0]);
+ thiscoord[1] = receivebits(buf, bitsizeint[1]);
+ thiscoord[2] = receivebits(buf, bitsizeint[2]);
+ } else {
+ receiveints(buf, 3, bitsize, sizeint, thiscoord);
+ }
+
+ i++;
+ thiscoord[0] += minint[0];
+ thiscoord[1] += minint[1];
+ thiscoord[2] += minint[2];
+
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+
+
+ flag = receivebits(buf, 1);
+ is_smaller = 0;
+ if (flag == 1) {
+ run = receivebits(buf, 5);
+ is_smaller = run % 3;
+ run -= is_smaller;
+ is_smaller--;
+ }
+ if (run > 0) {
+ thiscoord += 3;
+ for (k = 0; k < run; k+=3) {
+ receiveints(buf, 3, smallidx, sizesmall, thiscoord);
+ i++;
+ thiscoord[0] += prevcoord[0] - small;
+ thiscoord[1] += prevcoord[1] - small;
+ thiscoord[2] += prevcoord[2] - small;
+ if (k == 0) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
+ prevcoord[0] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
+ prevcoord[1] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
+ prevcoord[2] = tmp;
+ *lfp++ = prevcoord[0] * inv_precision;
+ *lfp++ = prevcoord[1] * inv_precision;
+ *lfp++ = prevcoord[2] * inv_precision;
+ } else {
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+ }
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
+ }
+ } else {
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
+ }
+ smallidx += is_smaller;
+ if (is_smaller < 0) {
+ small = smaller;
+ if (smallidx > FIRSTIDX) {
+ smaller = magicints[smallidx - 1] /2;
+ } else {
+ smaller = 0;
+ }
+ } else if (is_smaller > 0) {
+ smaller = small;
+ small = magicints[smallidx] / 2;
+ }
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
+ }
+ }
+ return 1;
+}
+
+
+
--- /dev/null
+/*____________________________________________________________________________
+ |
+ | libxdrf - portable fortran interface to xdr. some xdr routines
+ | are C routines for compressed coordinates
+ |
+ | version 1.1
+ |
+ | This collection of routines is intended to write and read
+ | data in a portable way to a file, so data written on one type
+ | of machine can be read back on a different type.
+ |
+ | all fortran routines use an integer 'xdrid', which is an id to the
+ | current xdr file, and is set by xdrfopen.
+ | most routines have in integer 'ret' which is the return value.
+ | The value of 'ret' is zero on failure, and most of the time one
+ | on succes.
+ |
+ | There are three routines useful for C users:
+ | xdropen(), xdrclose(), xdr3dfcoord().
+ | The first two replace xdrstdio_create and xdr_destroy, and *must* be
+ | used when you plan to use xdr3dfcoord(). (they are also a bit
+ | easier to interface). For writing data other than compressed coordinates
+ | you should use the standard C xdr routines (see xdr man page)
+ |
+ | xdrfopen(xdrid, filename, mode, ret)
+ | character *(*) filename
+ | character *(*) mode
+ |
+ | this will open the file with the given filename (string)
+ | and the given mode, it returns an id in xdrid, which is
+ | to be used in all other calls to xdrf routines.
+ | mode is 'w' to create, or update an file, for all other
+ | values of mode the file is opened for reading
+ |
+ | you need to call xdrfclose to flush the output and close
+ | the file.
+ | Note that you should not use xdrstdio_create, which comes with the
+ | standard xdr library
+ |
+ | xdrfclose(xdrid, ret)
+ | flush the data to the file, and closes the file;
+ | You should not use xdr_destroy (which comes standard with
+ | the xdr libraries.
+ |
+ | xdrfbool(xdrid, bp, ret)
+ | integer pb
+ |
+ | This filter produces values of either 1 or 0
+ |
+ | xdrfchar(xdrid, cp, ret)
+ | character cp
+ |
+ | filter that translate between characters and their xdr representation
+ | Note that the characters in not compressed and occupies 4 bytes.
+ |
+ | xdrfdouble(xdrid, dp, ret)
+ | double dp
+ |
+ | read/write a double.
+ |
+ | xdrffloat(xdrid, fp, ret)
+ | float fp
+ |
+ | read/write a float.
+ |
+ | xdrfint(xdrid, ip, ret)
+ | integer ip
+ |
+ | read/write integer.
+ |
+ | xdrflong(xdrid, lp, ret)
+ | integer lp
+ |
+ | this routine has a possible portablility problem due to 64 bits longs.
+ |
+ | xdrfshort(xdrid, sp, ret)
+ | integer *2 sp
+ |
+ | xdrfstring(xdrid, sp, maxsize, ret)
+ | character *(*)
+ | integer maxsize
+ |
+ | read/write a string, with maximum length given by maxsize
+ |
+ | xdrfwrapstring(xdris, sp, ret)
+ | character *(*)
+ |
+ | read/write a string (it is the same as xdrfstring accept that it finds
+ | the stringlength itself.
+ |
+ | xdrfvector(xdrid, cp, size, xdrfproc, ret)
+ | character *(*)
+ | integer size
+ | external xdrfproc
+ |
+ | read/write an array pointed to by cp, with number of elements
+ | defined by 'size'. the routine 'xdrfproc' is the name
+ | of one of the above routines to read/write data (like xdrfdouble)
+ | In contrast with the c-version you don't need to specify the
+ | byte size of an element.
+ | xdrfstring is not allowed here (it is in the c version)
+ |
+ | xdrf3dfcoord(xdrid, fp, size, precision, ret)
+ | real (*) fp
+ | real precision
+ | integer size
+ |
+ | this is *NOT* a standard xdr routine. I named it this way, because
+ | it invites people to use the other xdr routines.
+ | It is introduced to store specifically 3d coordinates of molecules
+ | (as found in molecular dynamics) and it writes it in a compressed way.
+ | It starts by multiplying all numbers by precision and
+ | rounding the result to integer. effectively converting
+ | all floating point numbers to fixed point.
+ | it uses an algorithm for compression that is optimized for
+ | molecular data, but could be used for other 3d coordinates
+ | as well. There is subtantial overhead involved, so call this
+ | routine only if you have a large number of coordinates to read/write
+ |
+ | ________________________________________________________________________
+ |
+ | Below are the routines to be used by C programmers. Use the 'normal'
+ | xdr routines to write integers, floats, etc (see man xdr)
+ |
+ | int xdropen(XDR *xdrs, const char *filename, const char *type)
+ | This will open the file with the given filename and the
+ | given mode. You should pass it an allocated XDR struct
+ | in xdrs, to be used in all other calls to xdr routines.
+ | Mode is 'w' to create, or update an file, and for all
+ | other values of mode the file is opened for reading.
+ | You need to call xdrclose to flush the output and close
+ | the file.
+ |
+ | Note that you should not use xdrstdio_create, which
+ | comes with the standard xdr library.
+ |
+ | int xdrclose(XDR *xdrs)
+ | Flush the data to the file, and close the file;
+ | You should not use xdr_destroy (which comes standard
+ | with the xdr libraries).
+ |
+ | int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
+ | This is \fInot\fR a standard xdr routine. I named it this
+ | way, because it invites people to use the other xdr
+ | routines.
+ |
+ | (c) 1995 Frans van Hoesel, hoesel@chem.rug.nl
+*/
+
+
+#include <limits.h>
+#include <malloc.h>
+#include <math.h>
+#include <rpc/rpc.h>
+#include <rpc/xdr.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "xdrf.h"
+
+int ftocstr(char *, int, char *, int);
+int ctofstr(char *, int, char *);
+
+#define MAXID 20
+static FILE *xdrfiles[MAXID];
+static XDR *xdridptr[MAXID];
+static char xdrmodes[MAXID];
+static unsigned int cnt;
+
+typedef void (* FUNCTION(xdrfproc)) (int *, void *, int *);
+
+void
+FUNCTION(xdrfbool) ARGS(`xdrid, pb, ret')
+int *xdrid, *ret;
+int *pb;
+{
+ *ret = xdr_bool(xdridptr[*xdrid], (bool_t *) pb);
+ cnt += sizeof(int);
+}
+
+void
+FUNCTION(xdrfchar) ARGS(`xdrid, cp, ret')
+int *xdrid, *ret;
+char *cp;
+{
+ *ret = xdr_char(xdridptr[*xdrid], cp);
+ cnt += sizeof(char);
+}
+
+void
+FUNCTION(xdrfdouble) ARGS(`xdrid, dp, ret')
+int *xdrid, *ret;
+double *dp;
+{
+ *ret = xdr_double(xdridptr[*xdrid], dp);
+ cnt += sizeof(double);
+}
+
+void
+FUNCTION(xdrffloat) ARGS(`xdrid, fp, ret')
+int *xdrid, *ret;
+float *fp;
+{
+ *ret = xdr_float(xdridptr[*xdrid], fp);
+ cnt += sizeof(float);
+}
+
+void
+FUNCTION(xdrfint) ARGS(`xdrid, ip, ret')
+int *xdrid, *ret;
+int *ip;
+{
+ *ret = xdr_int(xdridptr[*xdrid], ip);
+ cnt += sizeof(int);
+}
+
+void
+FUNCTION(xdrflong) ARGS(`xdrid, lp, ret')
+int *xdrid, *ret;
+long *lp;
+{
+ *ret = xdr_long(xdridptr[*xdrid], lp);
+ cnt += sizeof(long);
+}
+
+void
+FUNCTION(xdrfshort) ARGS(`xdrid, sp, ret')
+int *xdrid, *ret;
+short *sp;
+{
+ *ret = xdr_short(xdridptr[*xdrid], sp);
+ cnt += sizeof(sp);
+}
+
+void
+FUNCTION(xdrfuchar) ARGS(`xdrid, ucp, ret')
+int *xdrid, *ret;
+char *ucp;
+{
+ *ret = xdr_u_char(xdridptr[*xdrid], ucp);
+ cnt += sizeof(char);
+}
+
+void
+FUNCTION(xdrfulong) ARGS(`xdrid, ulp, ret')
+int *xdrid, *ret;
+unsigned long *ulp;
+{
+ *ret = xdr_u_long(xdridptr[*xdrid], ulp);
+ cnt += sizeof(unsigned long);
+}
+
+void
+FUNCTION(xdrfushort) ARGS(`xdrid, usp, ret')
+int *xdrid, *ret;
+unsigned short *usp;
+{
+ *ret = xdr_u_short(xdridptr[*xdrid], usp);
+ cnt += sizeof(unsigned short);
+}
+
+void
+FUNCTION(xdrf3dfcoord) ARGS(`xdrid, fp, size, precision, ret')
+int *xdrid, *ret;
+float *fp;
+int *size;
+float *precision;
+{
+ *ret = xdr3dfcoord(xdridptr[*xdrid], fp, size, precision);
+}
+
+void
+FUNCTION(xdrfstring) ARGS(`xdrid, STRING_ARG(sp), maxsize, ret')
+int *xdrid, *ret;
+STRING_ARG_DECL(sp);
+int *maxsize;
+{
+ char *tsp;
+
+ tsp = (char*) malloc(((STRING_LEN(sp)) + 1) * sizeof(char));
+ if (tsp == NULL) {
+ *ret = -1;
+ return;
+ }
+ if (ftocstr(tsp, *maxsize+1, STRING_PTR(sp), STRING_LEN(sp))) {
+ *ret = -1;
+ free(tsp);
+ return;
+ }
+ *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int) *maxsize);
+ ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
+ cnt += *maxsize;
+ free(tsp);
+}
+
+void
+FUNCTION(xdrfwrapstring) ARGS(`xdrid, STRING_ARG(sp), ret')
+int *xdrid, *ret;
+STRING_ARG_DECL(sp);
+{
+ char *tsp;
+ int maxsize;
+ maxsize = (STRING_LEN(sp)) + 1;
+ tsp = (char*) malloc(maxsize * sizeof(char));
+ if (tsp == NULL) {
+ *ret = -1;
+ return;
+ }
+ if (ftocstr(tsp, maxsize, STRING_PTR(sp), STRING_LEN(sp))) {
+ *ret = -1;
+ free(tsp);
+ return;
+ }
+ *ret = xdr_string(xdridptr[*xdrid], (char **) &tsp, (u_int)maxsize);
+ ctofstr( STRING_PTR(sp), STRING_LEN(sp), tsp);
+ cnt += maxsize;
+ free(tsp);
+}
+
+void
+FUNCTION(xdrfopaque) ARGS(`xdrid, cp, ccnt, ret')
+int *xdrid, *ret;
+caddr_t *cp;
+int *ccnt;
+{
+ *ret = xdr_opaque(xdridptr[*xdrid], (caddr_t)*cp, (u_int)*ccnt);
+ cnt += *ccnt;
+}
+
+void
+FUNCTION(xdrfsetpos) ARGS(`xdrid, pos, ret')
+int *xdrid, *ret;
+int *pos;
+{
+ *ret = xdr_setpos(xdridptr[*xdrid], (u_int) *pos);
+}
+
+void
+FUNCTION(xdrf) ARGS(`xdrid, pos')
+int *xdrid, *pos;
+{
+ *pos = xdr_getpos(xdridptr[*xdrid]);
+}
+
+void
+FUNCTION(xdrfvector) ARGS(`xdrid, cp, size, elproc, ret')
+int *xdrid, *ret;
+char *cp;
+int *size;
+FUNCTION(xdrfproc) elproc;
+{
+ int lcnt;
+ cnt = 0;
+ for (lcnt = 0; lcnt < *size; lcnt++) {
+ elproc(xdrid, (cp+cnt) , ret);
+ }
+}
+
+
+void
+FUNCTION(xdrfclose) ARGS(`xdrid, ret')
+int *xdrid;
+int *ret;
+{
+ *ret = xdrclose(xdridptr[*xdrid]);
+ cnt = 0;
+}
+
+void
+FUNCTION(xdrfopen) ARGS(`xdrid, STRING_ARG(fp), STRING_ARG(mode), ret')
+int *xdrid;
+STRING_ARG_DECL(fp);
+STRING_ARG_DECL(mode);
+int *ret;
+{
+ char fname[512];
+ char fmode[3];
+
+ if (ftocstr(fname, sizeof(fname), STRING_PTR(fp), STRING_LEN(fp))) {
+ *ret = 0;
+ }
+ if (ftocstr(fmode, sizeof(fmode), STRING_PTR(mode),
+ STRING_LEN(mode))) {
+ *ret = 0;
+ }
+
+ *xdrid = xdropen(NULL, fname, fmode);
+ if (*xdrid == 0)
+ *ret = 0;
+ else
+ *ret = 1;
+}
+
+/*___________________________________________________________________________
+ |
+ | what follows are the C routines for opening, closing xdr streams
+ | and the routine to read/write compressed coordinates together
+ | with some routines to assist in this task (those are marked
+ | static and cannot be called from user programs)
+*/
+#define MAXABS INT_MAX-2
+
+#ifndef MIN
+#define MIN(x,y) ((x) < (y) ? (x):(y))
+#endif
+#ifndef MAX
+#define MAX(x,y) ((x) > (y) ? (x):(y))
+#endif
+#ifndef SQR
+#define SQR(x) ((x)*(x))
+#endif
+static int magicints[] = {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
+ 80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
+ 812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
+ 8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
+ 82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
+ 832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304, 5284491, 6658042,
+ 8388607, 10568983, 13316085, 16777216 };
+
+#define FIRSTIDX 9
+/* note that magicints[FIRSTIDX-1] == 0 */
+#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
+
+
+/*__________________________________________________________________________
+ |
+ | xdropen - open xdr file
+ |
+ | This versions differs from xdrstdio_create, because I need to know
+ | the state of the file (read or write) so I can use xdr3dfcoord
+ | in eigther read or write mode, and the file descriptor
+ | so I can close the file (something xdr_destroy doesn't do).
+ |
+*/
+
+int xdropen(XDR *xdrs, const char *filename, const char *type) {
+ static int init_done = 0;
+ enum xdr_op lmode;
+ int xdrid;
+
+ if (init_done == 0) {
+ for (xdrid = 1; xdrid < MAXID; xdrid++) {
+ xdridptr[xdrid] = NULL;
+ }
+ init_done = 1;
+ }
+ xdrid = 1;
+ while (xdrid < MAXID && xdridptr[xdrid] != NULL) {
+ xdrid++;
+ }
+ if (xdrid == MAXID) {
+ return 0;
+ }
+ if (*type == 'w' || *type == 'W') {
+ type = "w+";
+ lmode = XDR_ENCODE;
+ } else {
+ type = "r";
+ lmode = XDR_DECODE;
+ }
+ xdrfiles[xdrid] = fopen(filename, type);
+ if (xdrfiles[xdrid] == NULL) {
+ xdrs = NULL;
+ return 0;
+ }
+ xdrmodes[xdrid] = *type;
+ /* next test isn't usefull in the case of C language
+ * but is used for the Fortran interface
+ * (C users are expected to pass the address of an already allocated
+ * XDR staructure)
+ */
+ if (xdrs == NULL) {
+ xdridptr[xdrid] = (XDR *) malloc(sizeof(XDR));
+ xdrstdio_create(xdridptr[xdrid], xdrfiles[xdrid], lmode);
+ } else {
+ xdridptr[xdrid] = xdrs;
+ xdrstdio_create(xdrs, xdrfiles[xdrid], lmode);
+ }
+ return xdrid;
+}
+
+/*_________________________________________________________________________
+ |
+ | xdrclose - close a xdr file
+ |
+ | This will flush the xdr buffers, and destroy the xdr stream.
+ | It also closes the associated file descriptor (this is *not*
+ | done by xdr_destroy).
+ |
+*/
+
+int xdrclose(XDR *xdrs) {
+ int xdrid;
+
+ if (xdrs == NULL) {
+ fprintf(stderr, "xdrclose: passed a NULL pointer\n");
+ exit(1);
+ }
+ for (xdrid = 1; xdrid < MAXID; xdrid++) {
+ if (xdridptr[xdrid] == xdrs) {
+
+ xdr_destroy(xdrs);
+ fclose(xdrfiles[xdrid]);
+ xdridptr[xdrid] = NULL;
+ return 1;
+ }
+ }
+ fprintf(stderr, "xdrclose: no such open xdr file\n");
+ exit(1);
+
+}
+
+/*____________________________________________________________________________
+ |
+ | sendbits - encode num into buf using the specified number of bits
+ |
+ | This routines appends the value of num to the bits already present in
+ | the array buf. You need to give it the number of bits to use and you
+ | better make sure that this number of bits is enough to hold the value
+ | Also num must be positive.
+ |
+*/
+
+static void sendbits(int buf[], int num_of_bits, int num) {
+
+ unsigned int cnt, lastbyte;
+ int lastbits;
+ unsigned char * cbuf;
+
+ cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
+ cnt = (unsigned int) buf[0];
+ lastbits = buf[1];
+ lastbyte =(unsigned int) buf[2];
+ while (num_of_bits >= 8) {
+ lastbyte = (lastbyte << 8) | ((num >> (num_of_bits -8)) /* & 0xff*/);
+ cbuf[cnt++] = lastbyte >> lastbits;
+ num_of_bits -= 8;
+ }
+ if (num_of_bits > 0) {
+ lastbyte = (lastbyte << num_of_bits) | num;
+ lastbits += num_of_bits;
+ if (lastbits >= 8) {
+ lastbits -= 8;
+ cbuf[cnt++] = lastbyte >> lastbits;
+ }
+ }
+ buf[0] = cnt;
+ buf[1] = lastbits;
+ buf[2] = lastbyte;
+ if (lastbits>0) {
+ cbuf[cnt] = lastbyte << (8 - lastbits);
+ }
+}
+
+/*_________________________________________________________________________
+ |
+ | sizeofint - calculate bitsize of an integer
+ |
+ | return the number of bits needed to store an integer with given max size
+ |
+*/
+
+static int sizeofint(const int size) {
+ unsigned int num = 1;
+ int num_of_bits = 0;
+
+ while (size >= num && num_of_bits < 32) {
+ num_of_bits++;
+ num <<= 1;
+ }
+ return num_of_bits;
+}
+
+/*___________________________________________________________________________
+ |
+ | sizeofints - calculate 'bitsize' of compressed ints
+ |
+ | given the number of small unsigned integers and the maximum value
+ | return the number of bits needed to read or write them with the
+ | routines receiveints and sendints. You need this parameter when
+ | calling these routines. Note that for many calls I can use
+ | the variable 'smallidx' which is exactly the number of bits, and
+ | So I don't need to call 'sizeofints for those calls.
+*/
+
+static int sizeofints( const int num_of_ints, unsigned int sizes[]) {
+ int i, num;
+ unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;
+ num_of_bytes = 1;
+ bytes[0] = 1;
+ num_of_bits = 0;
+ for (i=0; i < num_of_ints; i++) {
+ tmp = 0;
+ for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
+ tmp = bytes[bytecnt] * sizes[i] + tmp;
+ bytes[bytecnt] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ while (tmp != 0) {
+ bytes[bytecnt++] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ num_of_bytes = bytecnt;
+ }
+ num = 1;
+ num_of_bytes--;
+ while (bytes[num_of_bytes] >= num) {
+ num_of_bits++;
+ num *= 2;
+ }
+ return num_of_bits + num_of_bytes * 8;
+
+}
+
+/*____________________________________________________________________________
+ |
+ | sendints - send a small set of small integers in compressed format
+ |
+ | this routine is used internally by xdr3dfcoord, to send a set of
+ | small integers to the buffer.
+ | Multiplication with fixed (specified maximum ) sizes is used to get
+ | to one big, multibyte integer. Allthough the routine could be
+ | modified to handle sizes bigger than 16777216, or more than just
+ | a few integers, this is not done, because the gain in compression
+ | isn't worth the effort. Note that overflowing the multiplication
+ | or the byte buffer (32 bytes) is unchecked and causes bad results.
+ |
+ */
+
+static void sendints(int buf[], const int num_of_ints, const int num_of_bits,
+ unsigned int sizes[], unsigned int nums[]) {
+
+ int i;
+ unsigned int bytes[32], num_of_bytes, bytecnt, tmp;
+
+ tmp = nums[0];
+ num_of_bytes = 0;
+ do {
+ bytes[num_of_bytes++] = tmp & 0xff;
+ tmp >>= 8;
+ } while (tmp != 0);
+
+ for (i = 1; i < num_of_ints; i++) {
+ if (nums[i] >= sizes[i]) {
+ fprintf(stderr,"major breakdown in sendints num %d doesn't "
+ "match size %d\n", nums[i], sizes[i]);
+ exit(1);
+ }
+ /* use one step multiply */
+ tmp = nums[i];
+ for (bytecnt = 0; bytecnt < num_of_bytes; bytecnt++) {
+ tmp = bytes[bytecnt] * sizes[i] + tmp;
+ bytes[bytecnt] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ while (tmp != 0) {
+ bytes[bytecnt++] = tmp & 0xff;
+ tmp >>= 8;
+ }
+ num_of_bytes = bytecnt;
+ }
+ if (num_of_bits >= num_of_bytes * 8) {
+ for (i = 0; i < num_of_bytes; i++) {
+ sendbits(buf, 8, bytes[i]);
+ }
+ sendbits(buf, num_of_bits - num_of_bytes * 8, 0);
+ } else {
+ for (i = 0; i < num_of_bytes-1; i++) {
+ sendbits(buf, 8, bytes[i]);
+ }
+ sendbits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);
+ }
+}
+
+
+/*___________________________________________________________________________
+ |
+ | receivebits - decode number from buf using specified number of bits
+ |
+ | extract the number of bits from the array buf and construct an integer
+ | from it. Return that value.
+ |
+*/
+
+static int receivebits(int buf[], int num_of_bits) {
+
+ int cnt, num;
+ unsigned int lastbits, lastbyte;
+ unsigned char * cbuf;
+ int mask = (1 << num_of_bits) -1;
+
+ cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);
+ cnt = buf[0];
+ lastbits = (unsigned int) buf[1];
+ lastbyte = (unsigned int) buf[2];
+
+ num = 0;
+ while (num_of_bits >= 8) {
+ lastbyte = ( lastbyte << 8 ) | cbuf[cnt++];
+ num |= (lastbyte >> lastbits) << (num_of_bits - 8);
+ num_of_bits -=8;
+ }
+ if (num_of_bits > 0) {
+ if (lastbits < num_of_bits) {
+ lastbits += 8;
+ lastbyte = (lastbyte << 8) | cbuf[cnt++];
+ }
+ lastbits -= num_of_bits;
+ num |= (lastbyte >> lastbits) & ((1 << num_of_bits) -1);
+ }
+ num &= mask;
+ buf[0] = cnt;
+ buf[1] = lastbits;
+ buf[2] = lastbyte;
+ return num;
+}
+
+/*____________________________________________________________________________
+ |
+ | receiveints - decode 'small' integers from the buf array
+ |
+ | this routine is the inverse from sendints() and decodes the small integers
+ | written to buf by calculating the remainder and doing divisions with
+ | the given sizes[]. You need to specify the total number of bits to be
+ | used from buf in num_of_bits.
+ |
+*/
+
+static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
+ unsigned int sizes[], int nums[]) {
+ int bytes[32];
+ int i, j, num_of_bytes, p, num;
+
+ bytes[1] = bytes[2] = bytes[3] = 0;
+ num_of_bytes = 0;
+ while (num_of_bits > 8) {
+ bytes[num_of_bytes++] = receivebits(buf, 8);
+ num_of_bits -= 8;
+ }
+ if (num_of_bits > 0) {
+ bytes[num_of_bytes++] = receivebits(buf, num_of_bits);
+ }
+ for (i = num_of_ints-1; i > 0; i--) {
+ num = 0;
+ for (j = num_of_bytes-1; j >=0; j--) {
+ num = (num << 8) | bytes[j];
+ p = num / sizes[i];
+ bytes[j] = p;
+ num = num - p * sizes[i];
+ }
+ nums[i] = num;
+ }
+ nums[0] = bytes[0] | (bytes[1] << 8) | (bytes[2] << 16) | (bytes[3] << 24);
+}
+
+/*____________________________________________________________________________
+ |
+ | xdr3dfcoord - read or write compressed 3d coordinates to xdr file.
+ |
+ | this routine reads or writes (depending on how you opened the file with
+ | xdropen() ) a large number of 3d coordinates (stored in *fp).
+ | The number of coordinates triplets to write is given by *size. On
+ | read this number may be zero, in which case it reads as many as were written
+ | or it may specify the number if triplets to read (which should match the
+ | number written).
+ | Compression is achieved by first converting all floating numbers to integer
+ | using multiplication by *precision and rounding to the nearest integer.
+ | Then the minimum and maximum value are calculated to determine the range.
+ | The limited range of integers so found, is used to compress the coordinates.
+ | In addition the differences between succesive coordinates is calculated.
+ | If the difference happens to be 'small' then only the difference is saved,
+ | compressing the data even more. The notion of 'small' is changed dynamically
+ | and is enlarged or reduced whenever needed or possible.
+ | Extra compression is achieved in the case of GROMOS and coordinates of
+ | water molecules. GROMOS first writes out the Oxygen position, followed by
+ | the two hydrogens. In order to make the differences smaller (and thereby
+ | compression the data better) the order is changed into first one hydrogen
+ | then the oxygen, followed by the other hydrogen. This is rather special, but
+ | it shouldn't harm in the general case.
+ |
+ */
+
+int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) {
+
+
+ static int *ip = NULL;
+ static int oldsize;
+ static int *buf;
+
+ int minint[3], maxint[3], mindiff, *lip, diff;
+ int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;
+ int minidx, maxidx;
+ unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;
+ int flag, k;
+ int small, smaller, larger, i, is_small, is_smaller, run, prevrun;
+ float *lfp, lf;
+ int tmp, *thiscoord, prevcoord[3];
+ unsigned int tmpcoord[30];
+
+ int bufsize, xdrid, lsize;
+ unsigned int bitsize;
+ float inv_precision;
+ int errval = 1;
+
+ /* find out if xdrs is opened for reading or for writing */
+ xdrid = 0;
+ while (xdridptr[xdrid] != xdrs) {
+ xdrid++;
+ if (xdrid >= MAXID) {
+ fprintf(stderr, "xdr error. no open xdr stream\n");
+ exit (1);
+ }
+ }
+ if (xdrmodes[xdrid] == 'w') {
+
+ /* xdrs is open for writing */
+
+ if (xdr_int(xdrs, size) == 0)
+ return 0;
+ size3 = *size * 3;
+ /* when the number of coordinates is small, don't try to compress; just
+ * write them as floats using xdr_vector
+ */
+ if (*size <= 9 ) {
+ return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
+ (xdrproc_t)xdr_float));
+ }
+
+ xdr_float(xdrs, precision);
+ if (ip == NULL) {
+ ip = (int *)malloc(size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)malloc(bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ } else if (*size > oldsize) {
+ ip = (int *)realloc(ip, size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)realloc(buf, bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ }
+ /* buf[0-2] are special and do not contain actual data */
+ buf[0] = buf[1] = buf[2] = 0;
+ minint[0] = minint[1] = minint[2] = INT_MAX;
+ maxint[0] = maxint[1] = maxint[2] = INT_MIN;
+ prevrun = -1;
+ lfp = fp;
+ lip = ip;
+ mindiff = INT_MAX;
+ oldlint1 = oldlint2 = oldlint3 = 0;
+ while(lfp < fp + size3 ) {
+ /* find nearest integer */
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint1 = lf;
+ if (lint1 < minint[0]) minint[0] = lint1;
+ if (lint1 > maxint[0]) maxint[0] = lint1;
+ *lip++ = lint1;
+ lfp++;
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint2 = lf;
+ if (lint2 < minint[1]) minint[1] = lint2;
+ if (lint2 > maxint[1]) maxint[1] = lint2;
+ *lip++ = lint2;
+ lfp++;
+ if (*lfp >= 0.0)
+ lf = *lfp * *precision + 0.5;
+ else
+ lf = *lfp * *precision - 0.5;
+ if (fabs(lf) > MAXABS) {
+ /* scaling would cause overflow */
+ errval = 0;
+ }
+ lint3 = lf;
+ if (lint3 < minint[2]) minint[2] = lint3;
+ if (lint3 > maxint[2]) maxint[2] = lint3;
+ *lip++ = lint3;
+ lfp++;
+ diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);
+ if (diff < mindiff && lfp > fp + 3)
+ mindiff = diff;
+ oldlint1 = lint1;
+ oldlint2 = lint2;
+ oldlint3 = lint3;
+ }
+ xdr_int(xdrs, &(minint[0]));
+ xdr_int(xdrs, &(minint[1]));
+ xdr_int(xdrs, &(minint[2]));
+
+ xdr_int(xdrs, &(maxint[0]));
+ xdr_int(xdrs, &(maxint[1]));
+ xdr_int(xdrs, &(maxint[2]));
+
+ if ((float)maxint[0] - (float)minint[0] >= MAXABS ||
+ (float)maxint[1] - (float)minint[1] >= MAXABS ||
+ (float)maxint[2] - (float)minint[2] >= MAXABS) {
+ /* turning value in unsigned by subtracting minint
+ * would cause overflow
+ */
+ errval = 0;
+ }
+ sizeint[0] = maxint[0] - minint[0]+1;
+ sizeint[1] = maxint[1] - minint[1]+1;
+ sizeint[2] = maxint[2] - minint[2]+1;
+
+ /* check if one of the sizes is to big to be multiplied */
+ if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
+ bitsizeint[0] = sizeofint(sizeint[0]);
+ bitsizeint[1] = sizeofint(sizeint[1]);
+ bitsizeint[2] = sizeofint(sizeint[2]);
+ bitsize = 0; /* flag the use of large sizes */
+ } else {
+ bitsize = sizeofints(3, sizeint);
+ }
+ lip = ip;
+ luip = (unsigned int *) ip;
+ smallidx = FIRSTIDX;
+ while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
+ smallidx++;
+ }
+ xdr_int(xdrs, &smallidx);
+ maxidx = MIN(LASTIDX, smallidx + 8) ;
+ minidx = maxidx - 8; /* often this equal smallidx */
+ smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+ small = magicints[smallidx] / 2;
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
+ larger = magicints[maxidx] / 2;
+ i = 0;
+ while (i < *size) {
+ is_small = 0;
+ thiscoord = (int *)(luip) + i * 3;
+ if (smallidx < maxidx && i >= 1 &&
+ abs(thiscoord[0] - prevcoord[0]) < larger &&
+ abs(thiscoord[1] - prevcoord[1]) < larger &&
+ abs(thiscoord[2] - prevcoord[2]) < larger) {
+ is_smaller = 1;
+ } else if (smallidx > minidx) {
+ is_smaller = -1;
+ } else {
+ is_smaller = 0;
+ }
+ if (i + 1 < *size) {
+ if (abs(thiscoord[0] - thiscoord[3]) < small &&
+ abs(thiscoord[1] - thiscoord[4]) < small &&
+ abs(thiscoord[2] - thiscoord[5]) < small) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];
+ thiscoord[3] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];
+ thiscoord[4] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];
+ thiscoord[5] = tmp;
+ is_small = 1;
+ }
+
+ }
+ tmpcoord[0] = thiscoord[0] - minint[0];
+ tmpcoord[1] = thiscoord[1] - minint[1];
+ tmpcoord[2] = thiscoord[2] - minint[2];
+ if (bitsize == 0) {
+ sendbits(buf, bitsizeint[0], tmpcoord[0]);
+ sendbits(buf, bitsizeint[1], tmpcoord[1]);
+ sendbits(buf, bitsizeint[2], tmpcoord[2]);
+ } else {
+ sendints(buf, 3, bitsize, sizeint, tmpcoord);
+ }
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+ thiscoord = thiscoord + 3;
+ i++;
+
+ run = 0;
+ if (is_small == 0 && is_smaller == -1)
+ is_smaller = 0;
+ while (is_small && run < 8*3) {
+ if (is_smaller == -1 && (
+ SQR(thiscoord[0] - prevcoord[0]) +
+ SQR(thiscoord[1] - prevcoord[1]) +
+ SQR(thiscoord[2] - prevcoord[2]) >= smaller * smaller)) {
+ is_smaller = 0;
+ }
+
+ tmpcoord[run++] = thiscoord[0] - prevcoord[0] + small;
+ tmpcoord[run++] = thiscoord[1] - prevcoord[1] + small;
+ tmpcoord[run++] = thiscoord[2] - prevcoord[2] + small;
+
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+
+ i++;
+ thiscoord = thiscoord + 3;
+ is_small = 0;
+ if (i < *size &&
+ abs(thiscoord[0] - prevcoord[0]) < small &&
+ abs(thiscoord[1] - prevcoord[1]) < small &&
+ abs(thiscoord[2] - prevcoord[2]) < small) {
+ is_small = 1;
+ }
+ }
+ if (run != prevrun || is_smaller != 0) {
+ prevrun = run;
+ sendbits(buf, 1, 1); /* flag the change in run-length */
+ sendbits(buf, 5, run+is_smaller+1);
+ } else {
+ sendbits(buf, 1, 0); /* flag the fact that runlength did not change */
+ }
+ for (k=0; k < run; k+=3) {
+ sendints(buf, 3, smallidx, sizesmall, &tmpcoord[k]);
+ }
+ if (is_smaller != 0) {
+ smallidx += is_smaller;
+ if (is_smaller < 0) {
+ small = smaller;
+ smaller = magicints[smallidx-1] / 2;
+ } else {
+ smaller = small;
+ small = magicints[smallidx] / 2;
+ }
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
+ }
+ }
+ if (buf[1] != 0) buf[0]++;;
+ xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
+ return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
+ } else {
+
+ /* xdrs is open for reading */
+
+ if (xdr_int(xdrs, &lsize) == 0)
+ return 0;
+ if (*size != 0 && lsize != *size) {
+ fprintf(stderr, "wrong number of coordinates in xdr3dfcoor; "
+ "%d arg vs %d in file", *size, lsize);
+ }
+ *size = lsize;
+ size3 = *size * 3;
+ if (*size <= 9) {
+ return (xdr_vector(xdrs, (char *) fp, size3, sizeof(*fp),
+ (xdrproc_t)xdr_float));
+ }
+ xdr_float(xdrs, precision);
+ if (ip == NULL) {
+ ip = (int *)malloc(size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)malloc(bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ } else if (*size > oldsize) {
+ ip = (int *)realloc(ip, size3 * sizeof(*ip));
+ if (ip == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ bufsize = size3 * 1.2;
+ buf = (int *)realloc(buf, bufsize * sizeof(*buf));
+ if (buf == NULL) {
+ fprintf(stderr,"malloc failed\n");
+ exit(1);
+ }
+ oldsize = *size;
+ }
+ buf[0] = buf[1] = buf[2] = 0;
+
+ xdr_int(xdrs, &(minint[0]));
+ xdr_int(xdrs, &(minint[1]));
+ xdr_int(xdrs, &(minint[2]));
+
+ xdr_int(xdrs, &(maxint[0]));
+ xdr_int(xdrs, &(maxint[1]));
+ xdr_int(xdrs, &(maxint[2]));
+
+ sizeint[0] = maxint[0] - minint[0]+1;
+ sizeint[1] = maxint[1] - minint[1]+1;
+ sizeint[2] = maxint[2] - minint[2]+1;
+
+ /* check if one of the sizes is to big to be multiplied */
+ if ((sizeint[0] | sizeint[1] | sizeint[2] ) > 0xffffff) {
+ bitsizeint[0] = sizeofint(sizeint[0]);
+ bitsizeint[1] = sizeofint(sizeint[1]);
+ bitsizeint[2] = sizeofint(sizeint[2]);
+ bitsize = 0; /* flag the use of large sizes */
+ } else {
+ bitsize = sizeofints(3, sizeint);
+ }
+
+ xdr_int(xdrs, &smallidx);
+ maxidx = MIN(LASTIDX, smallidx + 8) ;
+ minidx = maxidx - 8; /* often this equal smallidx */
+ smaller = magicints[MAX(FIRSTIDX, smallidx-1)] / 2;
+ small = magicints[smallidx] / 2;
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
+ larger = magicints[maxidx];
+
+ /* buf[0] holds the length in bytes */
+
+ if (xdr_int(xdrs, &(buf[0])) == 0)
+ return 0;
+ if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
+ return 0;
+ buf[0] = buf[1] = buf[2] = 0;
+
+ lfp = fp;
+ inv_precision = 1.0 / * precision;
+ run = 0;
+ i = 0;
+ lip = ip;
+ while ( i < lsize ) {
+ thiscoord = (int *)(lip) + i * 3;
+
+ if (bitsize == 0) {
+ thiscoord[0] = receivebits(buf, bitsizeint[0]);
+ thiscoord[1] = receivebits(buf, bitsizeint[1]);
+ thiscoord[2] = receivebits(buf, bitsizeint[2]);
+ } else {
+ receiveints(buf, 3, bitsize, sizeint, thiscoord);
+ }
+
+ i++;
+ thiscoord[0] += minint[0];
+ thiscoord[1] += minint[1];
+ thiscoord[2] += minint[2];
+
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+
+
+ flag = receivebits(buf, 1);
+ is_smaller = 0;
+ if (flag == 1) {
+ run = receivebits(buf, 5);
+ is_smaller = run % 3;
+ run -= is_smaller;
+ is_smaller--;
+ }
+ if (run > 0) {
+ thiscoord += 3;
+ for (k = 0; k < run; k+=3) {
+ receiveints(buf, 3, smallidx, sizesmall, thiscoord);
+ i++;
+ thiscoord[0] += prevcoord[0] - small;
+ thiscoord[1] += prevcoord[1] - small;
+ thiscoord[2] += prevcoord[2] - small;
+ if (k == 0) {
+ /* interchange first with second atom for better
+ * compression of water molecules
+ */
+ tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];
+ prevcoord[0] = tmp;
+ tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];
+ prevcoord[1] = tmp;
+ tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];
+ prevcoord[2] = tmp;
+ *lfp++ = prevcoord[0] * inv_precision;
+ *lfp++ = prevcoord[1] * inv_precision;
+ *lfp++ = prevcoord[2] * inv_precision;
+ } else {
+ prevcoord[0] = thiscoord[0];
+ prevcoord[1] = thiscoord[1];
+ prevcoord[2] = thiscoord[2];
+ }
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
+ }
+ } else {
+ *lfp++ = thiscoord[0] * inv_precision;
+ *lfp++ = thiscoord[1] * inv_precision;
+ *lfp++ = thiscoord[2] * inv_precision;
+ }
+ smallidx += is_smaller;
+ if (is_smaller < 0) {
+ small = smaller;
+ if (smallidx > FIRSTIDX) {
+ smaller = magicints[smallidx - 1] /2;
+ } else {
+ smaller = 0;
+ }
+ } else if (is_smaller > 0) {
+ smaller = small;
+ small = magicints[smallidx] / 2;
+ }
+ sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
+ }
+ }
+ return 1;
+}
+
+
+
--- /dev/null
+divert(-1)
+undefine(`len')
+#
+# append an underscore to FORTRAN function names
+#
+define(`FUNCTION',`$1_')
+#
+# FORTRAN character strings are passed as follows:
+# a pointer to the base of the string is passed in the normal
+# argument list, and the length is passed by value as an extra
+# argument, after all of the other arguments.
+#
+define(`ARGS',`($1`'undivert(1))')
+define(`SAVE',`divert(1)$1`'divert(0)')
+define(`STRING_ARG',`$1_ptr`'SAVE(`, $1_len')')
+define(`STRING_ARG_DECL',`char * $1_ptr; int $1_len')
+define(`STRING_LEN',`$1_len')
+define(`STRING_PTR',`$1_ptr')
+divert(0)
--- /dev/null
+/*_________________________________________________________________
+ |
+ | xdrf.h - include file for C routines that want to use the
+ | functions below.
+*/
+
+int xdropen(XDR *xdrs, const char *filename, const char *type);
+int xdrclose(XDR *xdrs) ;
+int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) ;
+
--- /dev/null
+ subroutine xread(nazwa,ii,jj,kk,ll,mm,iR,ib,iparm)
+ implicit none
+ include "DIMENSIONS"
+ include "DIMENSIONS.ZSCOPT"
+ include "DIMENSIONS.FREE"
+ integer MaxTraj
+ parameter (MaxTraj=2050)
+#ifdef MPI
+ include "mpif.h"
+ integer IERROR,ERRCODE,STATUS(MPI_STATUS_SIZE)
+ include "COMMON.MPI"
+#endif
+ include "COMMON.CHAIN"
+ include "COMMON.IOUNITS"
+ include "COMMON.PROTFILES"
+ include "COMMON.NAMES"
+ include "COMMON.VAR"
+ include "COMMON.GEO"
+ include "COMMON.ENEPS"
+ include "COMMON.PROT"
+ include "COMMON.INTERACT"
+ include "COMMON.FREE"
+ include "COMMON.SBRIDGE"
+ include "COMMON.OBCINKA"
+ real*4 csingle(3,maxres2)
+ character*64 nazwa,bprotfile_temp
+ integer i,j,k,l,ii,jj(maxslice),kk(maxslice),ll(maxslice),
+ & mm(maxslice)
+ integer iscor,islice,islice1,slice
+ double precision energ
+ integer ilen,iroof
+ external ilen,iroof
+ double precision rmsdev,energia(0:max_ene),efree,eini,temp
+ double precision prop(maxQ)
+ integer ntot_all(0:maxprocs-1)
+ integer iparm,ib,iib,ir,nprop,nthr
+ double precision etot,time,ts(maxslice),te(maxslice)
+ integer is(maxslice),ie(maxslice),itraj,ntraj,it,iset
+ integer nstep(0:MaxTraj-1)
+ logical lerr
+
+ call set_slices(is,ie,ts,te,iR,ib,iparm)
+ do i=1,nQ
+ prop(i)=0.0d0
+ enddo
+ do i=0,MaxTraj-1
+ nstep(i)=0
+ enddo
+ ntraj=0
+ it=0
+ islice1=1
+ call opentmp(islice1,ientout,bprotfile_temp)
+ do while (.true.)
+ if (replica(iparm)) then
+ if (hamil_rep .or. umbrella(iparm)) then
+ read (ientin,*,end=1112,err=1112) time,eini,
+ & etot,temp,nss,(ihpb(j),jhpb(j),j=1,nss),
+ & nprop,(prop(j),j=1,nprop),iset
+ else
+ read (ientin,*,end=1112,err=1112) time,eini,
+ & etot,temp,nss,(ihpb(j),jhpb(j),j=1,nss),
+ & nprop,(prop(j),j=1,nprop)
+ endif
+ temp=1.0d0/(temp*1.987D-3)
+c write (iout,*) time,eini,etot,nss,
+c & (ihpb(j),jhpb(j),j=1,nss),(prop(j),j=1,nprop)
+c call flush(iout)
+ do i=1,nT_h(iparm)
+ if (beta_h(i,iparm).eq.temp) then
+ iib = i
+ goto 22
+ endif
+ enddo
+ 22 continue
+ if (i.gt.nT_h(iparm)) then
+ write (iout,*) "Error - temperature of conformation",
+ & ii,1.0d0/(temp*1.987D-3),
+ & " does not match any of the list"
+ write (iout,*)
+ & 1.0d0/(temp*1.987D-3),
+ & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+ call flush(iout)
+ call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
+ endif
+ else
+ read (ientin,*,end=1112,err=1112) time,eini,
+ & etot,nss,(ihpb(j),jhpb(j),j=1,nss),
+ & nprop,(prop(j),j=1,nprop)
+ iib = ib
+ endif
+ itraj=mod(it,totraj(iR,iparm))
+c write (*,*) "ii",ii," itraj",itraj
+c call flush(iout)
+ it=it+1
+ if (itraj.gt.ntraj) ntraj=itraj
+ nstep(itraj)=nstep(itraj)+1
+ islice=slice(nstep(itraj),time,is,ie,ts,te)
+ read (ientin,'(8f10.5)',end=1112,err=1112)
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct)
+ efree=0.0d0
+ if (islice.gt.0 .and. islice.le.nslice) then
+ ii=ii+1
+ kk(islice)=kk(islice)+1
+ mm(islice)=mm(islice)+1
+ if (mod(nstep(itraj),isampl(iparm)).eq.0) then
+ jj(islice)=jj(islice)+1
+ if (hamil_rep) then
+ snk(iR,iib,iset,islice)=snk(iR,iib,iset,islice)+1
+ else if (umbrella(iparm)) then
+ snk(iset,iib,iparm,islice)=snk(iset,iib,iparm,islice)+1
+ else
+ snk(iR,iib,iparm,islice)=snk(iR,iib,iparm,islice)+1
+ endif
+ ll(islice)=ll(islice)+1
+c write (iout,*) ii,kk,jj,ll,eini,(prop(j),j=1,nprop)
+#ifdef DEBUG
+c write (iout,*) "Writing conformation, record",ll(islice)
+c write (iout,*) "ib",ib," iib",iib
+ if (replica(iparm)) then
+ write (iout,*) "TEMP",1.0d0/(temp*1.987D-3)
+ write (iout,*) "TEMP list"
+ write (iout,*)
+ & (1.0d0/(beta_h(i,iparm)*1.987D-3),i=1,nT_h(iparm))
+ endif
+ call flush(iout)
+#endif
+c write (iout,*) "iparm",iparm," ib",ib," iR",iR," nQ",nQ
+c write (iout,*) "nres",nres," nnt",nnt," nct",nct," nss",nss
+c write (iout,*) "length",nres*4+(nct-nnt+1)*4+4+2*nss*4
+c call flush(iout)
+ if (islice.ne.islice1) then
+c write (iout,*) "islice",islice," islice1",islice1
+ close(ientout)
+c write (iout,*) "Closing file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+ call opentmp(islice,ientout,bprotfile_temp)
+c write (iout,*) "Opening file ",
+c & bprotfile_temp(:ilen(bprotfile_temp))
+c call flush(iout)
+ islice1=islice
+ endif
+ write(ientout,rec=ll(islice))
+ & ((csingle(l,k),l=1,3),k=1,nres),
+ & ((csingle(l,k+nres),l=1,3),k=nnt,nct),
+ & nss,(ihpb(k),jhpb(k),k=1,nss),
+ & eini,efree,rmsdev,(prop(i),i=1,nQ),iR,iib,iparm
+#ifdef DEBUG
+ do i=1,2*nres
+ do j=1,3
+ c(j,i)=csingle(j,i)
+ enddo
+ enddo
+ call int_from_cart1(.false.)
+ write (iout,*) "Writing conformation, record",ll(islice)
+ write (iout,*) "Cartesian coordinates"
+ write (iout,'(8f10.5)') ((c(j,i),j=1,3),i=1,nres)
+ write (iout,'(8f10.5)') ((c(j,i+nres),j=1,3),i=nnt,nct)
+ write (iout,*) "Internal coordinates"
+ write (iout,'(8f10.4)') (vbld(k),k=nnt+1,nct)
+ write (iout,'(8f10.4)') (vbld(k),k=nres+nnt,nres+nct)
+ write (iout,'(8f10.4)') (rad2deg*theta(k),k=3,nres)
+ write (iout,'(8f10.4)') (rad2deg*phi(k),k=4,nres)
+ write (iout,'(8f10.4)') (rad2deg*alph(k),k=2,nres-1)
+ write (iout,'(8f10.4)') (rad2deg*omeg(k),k=2,nres-1)
+ write (iout,'(16i5)') nss,(ihpb(k),jhpb(k),k=1,nss)
+c write (iout,'(8f10.5)') (prop(j),j=1,nQ)
+ write (iout,'(16i5)') iscor
+ call flush(iout)
+#endif
+ endif
+ endif
+ enddo
+ 1112 continue
+ close(ientout)
+ write (iout,'(i10," trajectories found in file.")') ntraj+1
+ write (iout,'(a)') "Numbers of steps in trajectories:"
+ write (iout,'(8i10)') (nstep(i),i=0,ntraj)
+ write (iout,*) ii," conformations read from file",
+ & nazwa(:ilen(nazwa))
+ write (iout,*) mm(islice)," conformations read so far, slice",
+ & islice
+ write (iout,*) ll(islice)," conformations stored so far, slice",
+ & islice
+ call flush(iout)
+ return
+ end
projects / unres.git / commitdiff