subroutine etotal(energia)
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
#ifndef ISNAN
external proc_proc
#ifdef MPI
include "mpif.h"
double precision weights_(n_ene)
+ double precision time00
+ integer ierror,ierr
#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.VAR'
- include 'COMMON.MD'
+c include 'COMMON.MD'
+ include 'COMMON.QRESTR'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.SPLITELE'
include 'COMMON.TORCNSTR'
+ include 'COMMON.SAXS'
+ double precision evdw,evdw1,evdw2,evdw2_14,ees,eel_loc,
+ & eello_turn3,eello_turn4,edfadis,estr,ehpb,ebe,ethetacnstr,
+ & escloc,etors,edihcnstr,etors_d,esccor,ecorr,ecorr5,ecorr6,eturn6,
+ & eliptran,Eafmforce,Etube,
+ & esaxs_constr,ehomology_constr,edfator,edfanei,edfabet
+ integer n_corr,n_corr1
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
weights_(21)=wsccor
weights_(22)=wtube
weights_(26)=wsaxs
+ weights_(28)=wdfa_dist
+ weights_(29)=wdfa_tor
+ weights_(30)=wdfa_nei
+ weights_(31)=wdfa_beta
C FG Master broadcasts the WEIGHTS_ array
call MPI_Bcast(weights_(1),n_ene,
& MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR)
wsccor=weights(21)
wtube=weights(22)
wsaxs=weights(26)
+ wdfa_dist=weights_(28)
+ wdfa_tor=weights_(29)
+ wdfa_nei=weights_(30)
+ wdfa_beta=weights_(31)
endif
time_Bcast=time_Bcast+MPI_Wtime()-time00
time_Bcastw=time_Bcastw+MPI_Wtime()-time00
c call chainbuild_cart
endif
+#ifndef DFA
+ edfadis=0.0d0
+ edfator=0.0d0
+ edfanei=0.0d0
+ edfabet=0.0d0
+#endif
c print *,'Processor',myrank,' calling etotal ipot=',ipot
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
#else
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
+#ifdef DFA
+C BARTEK for dfa test!
+ if (wdfa_dist.gt.0) then
+ call edfad(edfadis)
+ else
+ edfadis=0
+ endif
+c print*, 'edfad is finished!', edfadis
+ if (wdfa_tor.gt.0) then
+ call edfat(edfator)
+ else
+ edfator=0
+ endif
+c print*, 'edfat is finished!', edfator
+ if (wdfa_nei.gt.0) then
+ call edfan(edfanei)
+ else
+ edfanei=0
+ endif
+c print*, 'edfan is finished!', edfanei
+ if (wdfa_beta.gt.0) then
+ call edfab(edfabet)
+ else
+ edfabet=0
+ endif
+#endif
cmc
cmc Sep-06: egb takes care of dynamic ss bonds too
cmc
edihcnstr=0.0d0
if (ndih_constr.gt.0) call etor_constr(edihcnstr)
c print *,"Processor",myrank," computed Utor"
+ if (constr_homology.ge.1) then
+ call e_modeller(ehomology_constr)
+c print *,'iset=',iset,'me=',me,ehomology_constr,
+c & 'Processor',fg_rank,' CG group',kolor,
+c & ' absolute rank',MyRank
+ else
+ ehomology_constr=0.0d0
+ endif
C
C 6/23/01 Calculate double-torsional energy
C
else
esccor=0.0d0
endif
+#ifdef FOURBODY
C print *,"PRZED MULIt"
c print *,"Processor",myrank," computed Usccorr"
C
c & n_corr1
c call flush(iout)
endif
+#endif
c print *,"Processor",myrank," computed Ucorr"
c write (iout,*) "nsaxs",nsaxs," saxs_mode",saxs_mode
if (nsaxs.gt.0 .and. saxs_mode.eq.0) then
energia(24)=ethetacnstr
energia(25)=Etube
energia(26)=Esaxs_constr
+ energia(27)=ehomology_constr
+ energia(28)=edfadis
+ energia(29)=edfator
+ energia(30)=edfanei
+ energia(31)=edfabet
c write (iout,*) "esaxs_constr",energia(26)
c Here are the energies showed per procesor if the are more processors
c per molecule then we sum it up in sum_energy subroutine
end
c-------------------------------------------------------------------------------
subroutine sum_energy(energia,reduce)
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
#ifndef ISNAN
external proc_proc
#endif
#ifdef MPI
include "mpif.h"
+ integer ierr
+ double precision time00
#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
logical reduce
+ integer i
+ double precision evdw,evdw1,evdw2,evdw2_14,ees,eel_loc,
+ & eello_turn3,eello_turn4,edfadis,estr,ehpb,ebe,ethetacnstr,
+ & escloc,etors,edihcnstr,etors_d,esccor,ecorr,ecorr5,ecorr6,eturn6,
+ & eliptran,Eafmforce,Etube,
+ & esaxs_constr,ehomology_constr,edfator,edfanei,edfabet
+ double precision Uconst,etot
#ifdef MPI
if (nfgtasks.gt.1 .and. reduce) then
#ifdef DEBUG
ethetacnstr=energia(24)
Etube=energia(25)
esaxs_constr=energia(26)
+ ehomology_constr=energia(27)
+ edfadis=energia(28)
+ edfator=energia(29)
+ edfanei=energia(30)
+ edfabet=energia(31)
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1
& +wang*ebe+wtor*etors+wscloc*escloc
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+wumb*Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce
- & +ethetacnstr+wtube*Etube+wsaxs*esaxs_constr
+ & +ethetacnstr+wtube*Etube+wsaxs*esaxs_constr+ehomology_constr
+ & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
+ & +wdfa_beta*edfabet
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+wumb*Uconst+wsccor*esccor+wliptran*eliptran
& +Eafmforce
- & +ethetacnstr+wtube*Etube+wsaxs*esaxs_constr
+ & +ethetacnstr+wtube*Etube+wsaxs*esaxs_constr+ehomology_constr
+ & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
+ & +wdfa_beta*edfabet
#endif
energia(0)=etot
c detecting NaNQ
end
c-------------------------------------------------------------------------------
subroutine sum_gradient
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
#ifndef ISNAN
external proc_proc
#endif
#ifdef MPI
include 'mpif.h'
+ integer ierror,ierr
+ double precision time00,time01
#endif
double precision gradbufc(3,-1:maxres),gradbufx(3,-1:maxres),
& glocbuf(4*maxres),gradbufc_sum(3,-1:maxres)
include 'COMMON.TIME1'
include 'COMMON.MAXGRAD'
include 'COMMON.SCCOR'
+c include 'COMMON.MD'
+ include 'COMMON.QRESTR'
+ integer i,j,k
+ double precision scalar
+ double precision gvdwc_norm,gvdwc_scp_norm,gelc_norm,gvdwpp_norm,
+ &gradb_norm,ghpbc_norm,gradcorr_norm,gel_loc_norm,gcorr3_turn_norm,
+ &gcorr4_turn_norm,gradcorr5_norm,gradcorr6_norm,
+ &gcorr6_turn_norm,gsccorrc_norm,gscloc_norm,gvdwx_norm,
+ &gradx_scp_norm,ghpbx_norm,gradxorr_norm,gsccorrx_norm,
+ &gsclocx_norm
#ifdef TIMING
time01=MPI_Wtime()
#endif
& wstrain*ghpbc(j,i)
& +wliptran*gliptranc(j,i)
& +gradafm(j,i)
- & +welec*gshieldc(j,i)
- & +wcorr*gshieldc_ec(j,i)
- & +wturn3*gshieldc_t3(j,i)
- & +wturn4*gshieldc_t4(j,i)
- & +wel_loc*gshieldc_ll(j,i)
+ & +welec*gshieldc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
& +wtube*gg_tube(j,i)
& +wsaxs*gsaxsc(j,i)
-
-
-
enddo
enddo
#else
& +wel_loc*gshieldc_ll(j,i)
& +wtube*gg_tube(j,i)
& +wsaxs*gsaxsc(j,i)
-
-
-
enddo
enddo
#endif
+ do i=1,nct
+ do j=1,3
+ gradbufc(j,i)=gradbufc(j,i)+
+ & wdfa_dist*gdfad(j,i)+
+ & wdfa_tor*gdfat(j,i)+
+ & wdfa_nei*gdfan(j,i)+
+ & wdfa_beta*gdfab(j,i)
+ enddo
+ enddo
#ifdef DEBUG
write (iout,*) "gradc from gradbufc"
do i=1,nres
enddo
enddo
+ if (constr_homology.gt.0) then
+ do i=1,nct
+ do j=1,3
+ gradc(j,i,icg)=gradc(j,i,icg)+duscdiff(j,i)
+ gradx(j,i,icg)=gradx(j,i,icg)+duscdiffx(j,i)
+ enddo
+ enddo
+ endif
#ifdef DEBUG
write (iout,*) "gradc gradx gloc after adding"
do i=1,nres
gradcorr5_max=0.0d0
gradcorr6_max=0.0d0
gcorr6_turn_max=0.0d0
- gsccorc_max=0.0d0
+ gsccorrc_max=0.0d0
gscloc_max=0.0d0
gvdwx_max=0.0d0
gradx_scp_max=0.0d0
ghpbx_max=0.0d0
gradxorr_max=0.0d0
- gsccorx_max=0.0d0
+ gsccorrx_max=0.0d0
gsclocx_max=0.0d0
do i=1,nct
gvdwc_norm=dsqrt(scalar(gvdwc(1,i),gvdwc(1,i)))
if (gradcorr5_norm.gt.gradcorr5_max)
& gradcorr5_max=gradcorr5_norm
gradcorr6_norm=dsqrt(scalar(gradcorr6(1,i),gradcorr6(1,i)))
- if (gradcorr6_norm.gt.gradcorr6_max) gcorr6_max=gradcorr6_norm
+ if (gradcorr6_norm.gt.gradcorr6_max)gradcorr6_max=gradcorr6_norm
gcorr6_turn_norm=dsqrt(scalar(gcorr6_turn(1,i),
& gcorr6_turn(1,i)))
if (gcorr6_turn_norm.gt.gcorr6_turn_max)
& gcorr6_turn_max=gcorr6_turn_norm
- gsccorr_norm=dsqrt(scalar(gsccorc(1,i),gsccorc(1,i)))
- if (gsccorr_norm.gt.gsccorr_max) gsccorr_max=gsccorr_norm
+ gsccorrc_norm=dsqrt(scalar(gsccorc(1,i),gsccorc(1,i)))
+ if (gsccorrc_norm.gt.gsccorrc_max) gsccorrc_max=gsccorrc_norm
gscloc_norm=dsqrt(scalar(gscloc(1,i),gscloc(1,i)))
if (gscloc_norm.gt.gscloc_max) gscloc_max=gscloc_norm
gvdwx_norm=dsqrt(scalar(gvdwx(1,i),gvdwx(1,i)))
write (istat,'(1h#,21f10.2)') gvdwc_max,gvdwc_scp_max,
& gelc_max,gvdwpp_max,gradb_max,ghpbc_max,
& gradcorr_max,gel_loc_max,gcorr3_turn_max,gcorr4_turn_max,
- & gradcorr5_max,gradcorr6_max,gcorr6_turn_max,gsccorc_max,
+ & gradcorr5_max,gradcorr6_max,gcorr6_turn_max,gsccorrc_max,
& gscloc_max,gvdwx_max,gradx_scp_max,ghpbx_max,gradxorr_max,
- & gsccorx_max,gsclocx_max
+ & gsccorrx_max,gsclocx_max
close(istat)
if (gvdwc_max.gt.1.0d4) then
write (iout,*) "gvdwc gvdwx gradb gradbx"
end
c-------------------------------------------------------------------------------
subroutine rescale_weights(t_bath)
- implicit real*8 (a-h,o-z)
+ implicit none
+#ifdef MPI
+ include 'mpif.h'
+ integer ierror
+#endif
include 'DIMENSIONS'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.SBRIDGE'
include 'COMMON.CONTROL'
+ double precision t_bath
+ double precision facT,facT2,facT3,facT4,facT5
double precision kfac /2.4d0/
double precision x,x2,x3,x4,x5,licznik /1.12692801104297249644/
c facT=temp0/t_bath
end
C------------------------------------------------------------------------
subroutine enerprint(energia)
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.SBRIDGE'
- include 'COMMON.MD'
+ include 'COMMON.QRESTR'
double precision energia(0:n_ene)
+ double precision evdw,evdw1,evdw2,evdw2_14,ees,eel_loc,
+ & eello_turn3,eello_turn4,edfadis,estr,ehpb,ebe,ethetacnstr,
+ & escloc,etors,edihcnstr,etors_d,esccor,ecorr,ecorr5,ecorr6,
+ & eello_turn6,
+ & eliptran,Eafmforce,Etube,
+ & esaxs,ehomology_constr,edfator,edfanei,edfabet,etot
etot=energia(0)
evdw=energia(1)
evdw2=energia(2)
ethetacnstr=energia(24)
etube=energia(25)
esaxs=energia(26)
+ ehomology_constr=energia(27)
+C Bartek
+ edfadis = energia(28)
+ edfator = energia(29)
+ edfanei = energia(30)
+ edfabet = energia(31)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,
& estr,wbond,ebe,wang,
& escloc,wscloc,etors,wtor,etors_d,wtor_d,ehpb,wstrain,
+#ifdef FOURBODY
& ecorr,wcorr,
- & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
- & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,
- & ethetacnstr,ebr*nss,Uconst,wumb,eliptran,wliptran,Eafmforc,
- & etube,wtube,esaxs,wsaxs,
+ & ecorr5,wcorr5,ecorr6,wcorr6,
+#endif
+ & eel_loc,wel_loc,eello_turn3,wturn3,
+ & eello_turn4,wturn4,
+#ifdef FOURBODY
+ & eello_turn6,wturn6,
+#endif
+ & esccor,wsccor,edihcnstr,
+ & ethetacnstr,ebr*nss,Uconst,wumb,eliptran,wliptran,Eafmforce,
+ & etube,wtube,esaxs,wsaxs,ehomology_constr,
+ & edfadis,wdfa_dist,edfator,wdfa_tor,edfanei,wdfa_nei,
+ & edfabet,wdfa_beta,
& 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)'/
- & '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,
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/
+ & 'EVDWPP=',1pE16.6,' WEIGHT=',1pE16.6,' (p-p VDW)'/
+ & 'ESTR= ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/
+ & 'EHBP= ',1pE16.6,' WEIGHT=',1pE16.6,
& ' (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)'/
+#ifdef FOURBODY
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+#endif
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/
+#ifdef FOURBODY
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/
+#endif
+ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (virtual-bond dihedral angle restraints)'/
& 'ETHETC=',1pE16.6,' (virtual-bond angle restraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
- & 'UCONST=',1pE16.6,' WEIGHT=',1pD16.6' (umbrella restraints)'/
- & 'ELT= ',1pE16.6,' WEIGHT=',1pD16.6,' (Lipid transfer)'/
+ & 'UCONST=',1pE16.6,' WEIGHT=',1pE16.6' (umbrella restraints)'/
+ & 'ELT= ',1pE16.6,' WEIGHT=',1pE16.6,' (Lipid transfer)'/
& 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/
- & 'ETUBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (tube confinment)'/
- & 'E_SAXS=',1pE16.6,' WEIGHT=',1pD16.6,' (SAXS restraints)'/
+ & 'ETUBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (tube confinment)'/
+ & 'E_SAXS=',1pE16.6,' WEIGHT=',1pE16.6,' (SAXS restraints)'/
+ & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/
+ & 'EDFAD= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA distance energy)'/
+ & 'EDFAT= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA torsion energy)'/
+ & 'EDFAN= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA NCa energy)'/
+ & 'EDFAB= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA Beta energy)'/
& 'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,
& estr,wbond,ebe,wang,
& escloc,wscloc,etors,wtor,etors_d,wtor_d,ehpb,wstrain,
+#ifdef FOURBODY
& ecorr,wcorr,
- & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,
- & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr,
+ & ecorr5,wcorr5,ecorr6,wcorr6,
+#endif
+ & eel_loc,wel_loc,eello_turn3,wturn3,
+ & eello_turn4,wturn4,
+#ifdef FOURBODY
+ & eello_turn6,wturn6,
+#endif
+ & esccor,wsccor,edihcnstr,
& ethetacnstr,ebr*nss,Uconst,wumb,eliptran,wliptran,Eafmforc,
- & etube,wtube,esaxs,wsaxs,
+ & etube,wtube,esaxs,wsaxs,ehomology_constr,
+ & edfadis,wdfa_dist,edfator,wdfa_tor,edfanei,wdfa_nei,
+ & edfabet,wdfa_beta,
& 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,
+ & 'EVDW= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-SC)'/
+ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC-p)'/
+ & 'EES= ',1pE16.6,' WEIGHT=',1pE16.6,' (p-p)'/
+ & 'ESTR= ',1pE16.6,' WEIGHT=',1pE16.6,' (stretching)'/
+ & 'EBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (bending)'/
+ & 'ESC= ',1pE16.6,' WEIGHT=',1pE16.6,' (SC local)'/
+ & 'ETORS= ',1pE16.6,' WEIGHT=',1pE16.6,' (torsional)'/
+ & 'ETORSD=',1pE16.6,' WEIGHT=',1pE16.6,' (double torsional)'/
+ & 'EHBP= ',1pE16.6,' WEIGHT=',1pE16.6,
& ' (SS bridges & dist. restr.)'/
- & '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)'/
+#ifdef FOURBODY
+ & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+ & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/
+#endif
+ & 'EELLO= ',1pE16.6,' WEIGHT=',1pE16.6,' (electrostatic-local)'/
+ & 'ETURN3=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 3rd order)'/
+ & 'ETURN4=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 4th order)'/
+#ifdef FOURBODY
+ & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/
+#endif
+ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/
& 'EDIHC= ',1pE16.6,' (virtual-bond dihedral angle restraints)'/
& 'ETHETC=',1pE16.6,' (virtual-bond angle restraints)'/
& 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
- & 'UCONST=',1pE16.6,' WEIGHT=',1pD16.6' (umbrella restraints)'/
- & 'ELT= ',1pE16.6,' WEIGHT=',1pD16.6,' (Lipid transfer)'/
+ & 'UCONST=',1pE16.6,' WEIGHT=',1pE16.6' (umbrella restraints)'/
+ & 'ELT= ',1pE16.6,' WEIGHT=',1pE16.6,' (Lipid transfer)'/
& 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/
- & 'ETUBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (tube confinment)'/
- & 'E_SAXS=',1pE16.6,' WEIGHT=',1pD16.6,' (SAXS restraints)'/
+ & 'ETUBE= ',1pE16.6,' WEIGHT=',1pE16.6,' (tube confinment)'/
+ & 'E_SAXS=',1pE16.6,' WEIGHT=',1pE16.6,' (SAXS restraints)'/
+ & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/
+ & 'EDFAD= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA distance energy)'/
+ & 'EDFAT= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA torsion energy)'/
+ & 'EDFAN= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA NCa energy)'/
+ & 'EDFAB= ',1pE16.6,' WEIGHT=',1pE16.6,' (DFA Beta energy)'/
& 'ETOT= ',1pE16.6,' (total)')
#endif
return
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)
+ implicit none
+ double precision accur
include 'DIMENSIONS'
parameter (accur=1.0d-10)
include 'COMMON.GEO'
include 'COMMON.SBRIDGE'
include 'COMMON.NAMES'
include 'COMMON.IOUNITS'
+ include 'COMMON.SPLITELE'
+#ifdef FOURBODY
include 'COMMON.CONTACTS'
- dimension gg(3)
+ include 'COMMON.CONTMAT'
+#endif
+ double precision gg(3)
+ double precision evdw,evdwij
+ integer i,j,k,itypi,itypj,itypi1,num_conti,iint
+ double precision xi,yi,zi,xj,yj,zj,rij,eps0ij,fac,e1,e2,rrij,
+ & sigij,r0ij,rcut,sqrij,sss1,sssgrad1
+ double precision fcont,fprimcont
+ double precision sscale,sscagrad
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
C Change 12/1/95 to calculate four-body interactions
rij=xj*xj+yj*yj+zj*zj
rrij=1.0D0/rij
+ sqrij=dsqrt(rij)
+ sss1=sscale(sqrij,r_cut_int)
+ if (sss1.eq.0.0d0) cycle
+ sssgrad1=sscagrad(sqrij,r_cut_int)
+
c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
cd & restyp(itypi),i,restyp(itypj),j,a(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
+ evdw=evdw+sss1*evdwij
C
C Calculate the components of the gradient in DC and X
C
fac=-rrij*(e1+evdwij)
+ & +evdwij*sssgrad1/sqrij
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
cgrad enddo
cgrad enddo
C
+#ifdef FOURBODY
C 12/1/95, revised on 5/20/97
C
C Calculate the contact function. The ith column of the array JCONT will
cd & i,j,(gacont(kk,num_conti,i),kk=1,3)
endif
endif
+#endif
enddo ! j
enddo ! iint
C Change 12/1/95
+#ifdef FOURBODY
num_cont(i)=num_conti
+#endif
enddo ! i
do i=1,nct
do j=1,3
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)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
- dimension gg(3)
+ include 'COMMON.SPLITELE'
+ double precision gg(3)
+ double precision evdw,evdwij
+ integer i,j,k,itypi,itypj,itypi1,iint
+ double precision xi,yi,zi,xj,yj,zj,rij,eps0ij,fac,e1,e2,rrij,
+ & fac_augm,e_augm,r_inv_ij,r_shift_inv,sss1,sssgrad1
logical scheck
+ double precision sscale,sscagrad
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
e_augm=augm(itypi,itypj)*fac_augm
r_inv_ij=dsqrt(rrij)
rij=1.0D0/r_inv_ij
+ sss1=sscale(rij,r_cut_int)
+ if (sss1.eq.0.0d0) cycle
+ sssgrad1=sscagrad(rij,r_cut_int)
r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
fac=r_shift_inv**expon
C have you changed here?
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)
+ & +evdwij*sssgrad1*r_inv_ij
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
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)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SPLITELE'
+ integer icall
common /srutu/ icall
+ double precision evdw
+ integer itypi,itypj,itypi1,iint,ind
+ double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,xi,yi,zi,
+ & sss1,sssgrad1
+ double precision sscale,sscagrad
c double precision rrsave(maxdim)
logical lprn
evdw=0.0D0
cd rrij=rrsave(ind)
cd endif
rij=dsqrt(rrij)
+ sss1=sscale(1.0d0/rij,r_cut_int)
+ if (sss1.eq.0.0d0) cycle
+ sssgrad1=sscagrad(1.0d0/rij,r_cut_int)
C Calculate the angle-dependent terms of energy & contributions to derivatives.
call sc_angular
C Calculate whole angle-dependent part of epsilon and contributions
fac=-expon*(e1+evdwij)
sigder=fac/sigsq
fac=rrij*fac
+ & +evdwij*sssgrad1*rij
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
+ call sc_grad_scale(sss1)
enddo ! j
enddo ! iint
enddo ! i
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)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.SPLITELE'
include 'COMMON.SBRIDGE'
logical lprn
- integer xshift,yshift,zshift
-
+ integer xshift,yshift,zshift,subchap
+ double precision evdw
+ integer itypi,itypj,itypi1,iint,ind
+ double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,xi,yi,zi
+ double precision fracinbuf,sslipi,evdwij_przed_tri,sig0ij,
+ & sslipj,ssgradlipj,ssgradlipi,dist_init,xj_safe,yj_safe,zj_safe,
+ & xj_temp,yj_temp,zj_temp,dist_temp,sig,rij_shift,faclip
+ double precision dist,sscale,sscagrad,sscagradlip,sscalelip
evdw=0.0D0
ccccc energy_dec=.false.
C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
c & dc_norm(1,nres+j),dc_norm(2,nres+j),dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
- sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
- sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
-
+ sss=sscale(1.0d0/rij,r_cut_int)
c write (iout,'(a7,4f8.3)')
c & "ssscale",sss,((1.0d0/rij)/sigma(itypi,itypj)),r_cut,rlamb
- if (sss.gt.0.0d0) then
+ if (sss.eq.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/rij,r_cut_int)
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
call sc_angular
& evdwij
endif
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'evdw',i,j,evdwij
+ if (energy_dec) write (iout,'(a,2i5,3f10.5)')
+ & 'r sss evdw',i,j,rij,sss,evdwij
C Calculate gradient components.
e1=e1*eps1*eps2rt**2*eps3rt**2
fac=rij*fac
c print '(2i4,6f8.4)',i,j,sss,sssgrad*
c & evdwij,fac,sigma(itypi,itypj),expon
- fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
+ fac=fac+evdwij*sssgrad*rij
c fac=0.0d0
C Calculate the radial part of the gradient
gg_lipi(3)=eps1*(eps2rt*eps2rt)
- &*(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
- & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
- &+faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
+ & *(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
+ & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
+ & +faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
gg_lipj(3)=ssgradlipj*gg_lipi(3)
gg_lipi(3)=gg_lipi(3)*ssgradlipi
C gg_lipi(3)=0.0d0
gg(2)=yj*fac
gg(3)=zj*fac
C Calculate angular part of the gradient.
- call sc_grad
- endif
+ call sc_grad_scale(sss)
ENDIF ! dyn_ss
enddo ! j
enddo ! iint
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)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
- integer xshift,yshift,zshift
+ include 'COMMON.SPLITELE'
+ integer xshift,yshift,zshift,subchap
+ integer icall
common /srutu/ icall
logical lprn
+ double precision evdw
+ integer itypi,itypj,itypi1,iint,ind
+ double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,r0ij,
+ & xi,yi,zi,fac_augm,e_augm
+ double precision fracinbuf,sslipi,evdwij_przed_tri,sig0ij,
+ & sslipj,ssgradlipj,ssgradlipi,dist_init,xj_safe,yj_safe,zj_safe,
+ & xj_temp,yj_temp,zj_temp,dist_temp,sig,rij_shift,faclip,sssgrad1
+ double precision dist,sscale,sscagrad,sscagradlip,sscalelip
evdw=0.0D0
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
dzj=dc_norm(3,nres+j)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale(1.0d0/rij,r_cut_int)
+ if (sss.eq.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/rij,r_cut_int)
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
call sc_angular
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac-2*expon*rrij*e_augm
- fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
+ fac=fac+(evdwij+e_augm)*sssgrad*rij
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
+ call sc_grad_scale(sss)
enddo ! j
enddo ! iint
enddo ! i
include 'COMMON.SBRIDGE'
include 'COMMON.NAMES'
include 'COMMON.IOUNITS'
- include 'COMMON.CONTACTS'
+c include 'COMMON.CONTACTS'
dimension gg(3)
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
- include 'COMMON.CONTACTS'
+c include 'COMMON.CONTACTS'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
zj=zj_safe-zmedi
endif
rij=xj*xj+yj*yj+zj*zj
- sss=sscale(sqrt(rij))
- sssgrad=sscagrad(sqrt(rij))
+ sss=sscale(sqrt(rij),r_cut_int)
+ sssgrad=sscagrad(sqrt(rij),r_cut_int)
if (rij.lt.r0ijsq) then
evdw1ij=0.25d0*(rij-r0ijsq)**2
fac=rij-r0ijsq
#endif
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
- 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 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
- include 'COMMON.CONTACTS'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
#else
do i=3,nres+1
#endif
- if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ ii=ireschain(i-2)
+c write (iout,*) "i",i,i-2," ii",ii
+ if (ii.eq.0) cycle
+ innt=chain_border(1,ii)
+ inct=chain_border(2,ii)
+c write (iout,*) "i",i,i-2," ii",ii," innt",innt," inct",inct
+c if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ if (i.gt. innt+2 .and. i.lt.inct+2) then
iti = itype2loc(itype(i-2))
else
iti=nloctyp
endif
c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
- if (i.gt. nnt+1 .and. i.lt.nct+1) then
+ if (i.gt. innt+1 .and. i.lt.inct+1) then
iti1 = itype2loc(itype(i-1))
else
iti1=nloctyp
endif
-c write(iout,*),i
+c write(iout,*),"i",i,i-2," iti",itype(i-2),iti,
+c & " iti1",itype(i-1),iti1
#ifdef NEWCORR
cost1=dcos(theta(i-1))
sint1=dsin(theta(i-1))
write (iout,*) 'theta=', theta(i-1)
#endif
#else
- if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ if (i.gt. innt+2 .and. i.lt.inct+2) then
+c if (i.gt. nnt+2 .and. i.lt.nct+2) then
iti = itype2loc(itype(i-2))
else
iti=nloctyp
write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
#endif
enddo
+ mu=0.0d0
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
do i=3,nres+1
#endif
- if (i .lt. nres+1) then
+c if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle
+ if (i .lt. nres+1 .and. itype(i-1).lt.ntyp1) then
sin1=dsin(phi(i))
cos1=dcos(phi(i))
sintab(i-2)=sin1
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
+ if (i .gt. 3) then
obrot_der(1,i-2)=-sin1
obrot_der(2,i-2)= cos1
Ugder(1,1,i-2)= sin1
Ug2der(2,2,i-2)=0.0d0
endif
c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
- if (i.gt. nnt+2 .and. i.lt.nct+2) then
+c if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ if (i.gt.nnt+2 .and.i.lt.nct+2) then
iti = itype2loc(itype(i-2))
else
iti=nloctyp
c write(iout,*) "Macierz EUG",
c & eug(1,1,i-2),eug(1,2,i-2),eug(2,1,i-2),
c & eug(2,2,i-2)
+#ifdef FOURBODY
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0)
& then
call matmat2(CC(1,1,i-2),Ug(1,1,i-2),CUg(1,1,i-2))
call matvec2(Ctilde(1,1,i-1),obrot(1,i-2),Ctobr(1,i-2))
call matvec2(Dtilde(1,1,i-2),obrot2(1,i-2),Dtobr2(1,i-2))
endif
+#endif
else
do k=1,2
Ub2(k,i-2)=0.0d0
cd write (iout,*) 'mu1',mu1(:,i-2)
cd write (iout,*) 'mu2',mu2(:,i-2)
cd write (iout,*) 'mu',i-2,mu(:,i-2)
+#ifdef FOURBODY
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
& then
call matmat2(CC(1,1,i-1),Ugder(1,1,i-2),CUgder(1,1,i-2))
call matmat2(EUg(1,1,i-2),DD(1,1,i-1),EUgD(1,1,i-2))
call matmat2(EUgder(1,1,i-2),DD(1,1,i-1),EUgDder(1,1,i-2))
endif
+#endif
enddo
+#ifdef FOURBODY
C Matrices dependent on two consecutive virtual-bond dihedrals.
C The order of matrices is from left to right.
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i))
enddo
endif
+#endif
#if defined(MPI) && defined(PARMAT)
#ifdef DEBUG
c if (fg_rank.eq.0) then
call MPI_Allgatherv(sintab2(ivec_start),ivec_count(fg_rank1),
& MPI_DOUBLE_PRECISION,sintab2(1),ivec_count(0),ivec_displ(0),
& MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
+#ifdef FOURBODY
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0)
& then
call MPI_Allgatherv(Ctobr(1,ivec_start),ivec_count(fg_rank1),
& MPI_MAT2,Ug2DtEUgder(1,1,1,1),ivec_count(0),ivec_displ(0),
& MPI_MAT2,FG_COMM1,IERR)
endif
+#endif
#else
c Passes matrix info through the ring
isend=fg_rank1
& iprev,6600+irecv,FG_COMM,status,IERR)
c write (iout,*) "Gather PRECOMP12"
c call flush(iout)
+#ifdef FOURBODY
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0)
& then
call MPI_SENDRECV(ug2db1t(1,ivec_displ(isend)+1),1,
& Ug2DtEUgder(1,1,1,ivec_displ(irecv)+1),1,
& MPI_PRECOMP23(lenrecv),
& iprev,9900+irecv,FG_COMM,status,IERR)
+#endif
c write (iout,*) "Gather PRECOMP23"
c call flush(iout)
endif
cd enddo
return
end
-C--------------------------------------------------------------------------
+C-----------------------------------------------------------------------------
subroutine eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
C
C This subroutine calculates the average interaction energy and its gradient
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
+#ifdef FOURBODY
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+#endif
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
eello_turn3=0.0d0
eello_turn4=0.0d0
ind=0
+#ifdef FOURBODY
do i=1,nres
num_cont_hb(i)=0
enddo
+#endif
cd print '(a)','Enter EELEC'
cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
do i=1,nres
num_conti=0
call eelecij(i,i+2,ees,evdw1,eel_loc)
if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
+#ifdef FOURBODY
num_cont_hb(i)=num_conti
+#endif
enddo
do i=iturn4_start,iturn4_end
if (i.lt.1) cycle
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+#ifdef FOURBODY
num_conti=num_cont_hb(i)
+#endif
c write(iout,*) "JESTEM W PETLI"
call eelecij(i,i+3,ees,evdw1,eel_loc)
if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
& call eturn4(i,eello_turn4)
+#ifdef FOURBODY
num_cont_hb(i)=num_conti
+#endif
enddo ! i
C Loop over all neighbouring boxes
C do xshift=-1,1
c endif
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
+#ifdef FOURBODY
num_conti=num_cont_hb(i)
+#endif
C I TU KURWA
do j=ielstart(i),ielend(i)
C do j=16,17
&) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
+#ifdef FOURBODY
num_cont_hb(i)=num_conti
+#endif
enddo ! i
C enddo ! zshift
C enddo ! yshift
end
C-------------------------------------------------------------------------------
subroutine eelecij(i,j,ees,evdw1,eel_loc)
- implicit real*8 (a-h,o-z)
+ implicit none
include 'DIMENSIONS'
#ifdef MPI
include "mpif.h"
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
+#ifdef FOURBODY
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+#endif
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.TIME1'
include 'COMMON.SPLITELE'
include 'COMMON.SHIELD'
- dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
+ double precision 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),gmuij1(4),gmuji1(4),
& gmuij2(4),gmuji2(4)
+ double precision dxi,dyi,dzi
+ double precision dx_normi,dy_normi,dz_normi,aux
+ integer j1,j2,lll,num_conti
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
& dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
& num_conti,j1,j2
+ integer k,i,j,iteli,itelj,kkk,l,kkll,m,isubchap,ilist,iresshield
+ double precision ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp
+ double precision ees,evdw1,eel_loc,aaa,bbb,ael3i
+ double precision dxj,dyj,dzj,dx_normj,dy_normj,dz_normj,xj,yj,zj,
+ & rij,r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,
+ & evdwij,el1,el2,eesij,ees0ij,facvdw,facel,fac1,ecosa,
+ & ecosb,ecosg,ury,urz,vry,vrz,facr,a22der,a23der,a32der,
+ & a33der,eel_loc_ij,cosa4,wij,cosbg1,cosbg2,ees0pij,
+ & ees0pij1,ees0mij,ees0mij1,fac3p,ees0mijp,ees0pijp,
+ & ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,
+ & ecosgp,ecosam,ecosbm,ecosgm,ghalf,rlocshield
+ double precision a22,a23,a32,a33,geel_loc_ij,geel_loc_ji
+ double precision dist_init,xj_safe,yj_safe,zj_safe,
+ & xj_temp,yj_temp,zj_temp,dist_temp,xmedi,ymedi,zmedi
+ double precision sscale,sscagrad,scalar
+
c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
#ifdef MOMENT
double precision scal_el /1.0d0/
C zj=zj-zmedi
rij=xj*xj+yj*yj+zj*zj
- sss=sscale(sqrt(rij))
- sssgrad=sscagrad(sqrt(rij))
+ sss=sscale(sqrt(rij),r_cut_int)
+ if (sss.eq.0.0d0) return
+ sssgrad=sscagrad(sqrt(rij),r_cut_int)
c if (sss.gt.0.0d0) then
rrmij=1.0D0/rij
rij=dsqrt(rij)
fac_shield(i)=1.0
fac_shield(j)=1.0
eesij=(el1+el2)
- ees=ees+eesij
+ ees=ees+eesij*sss
endif
evdw1=evdw1+evdwij*sss
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & xmedi,ymedi,zmedi,xj,yj,zj
if (energy_dec) then
- write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)')
- &'evdw1',i,j,evdwij
- &,iteli,itelj,aaa,evdw1,sss
- write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
- &fac_shield(i),fac_shield(j)
+ write (iout,'(a6,2i5,0pf7.3,2i5,e11.3,3f10.5)')
+ & 'evdw1',i,j,evdwij,iteli,itelj,aaa,evdw1,sss,rij
+ write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
+ & fac_shield(i),fac_shield(j)
endif
C
*
* Radial derivatives. First process both termini of the fragment (i,j)
*
+ aux=facel+sssgrad*eesij
ggg(1)=facel*xj
ggg(2)=facel*yj
ggg(3)=facel*zj
iresshield=shield_list(ilist,j)
do k=1,3
rlocshield=grad_shield_side(k,ilist,j)*eesij/fac_shield(j)
- & *2.0
+ & *2.0*sss
gshieldx(k,iresshield)=gshieldx(k,iresshield)+
& rlocshield
- & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0
+ & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0*sss
gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield
C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)
do k=1,3
gshieldc(k,i)=gshieldc(k,i)+
- & grad_shield(k,i)*eesij/fac_shield(i)*2.0
+ & grad_shield(k,i)*eesij/fac_shield(i)*2.0*sss
gshieldc(k,j)=gshieldc(k,j)+
- & grad_shield(k,j)*eesij/fac_shield(j)*2.0
+ & grad_shield(k,j)*eesij/fac_shield(j)*2.0*sss
gshieldc(k,i-1)=gshieldc(k,i-1)+
- & grad_shield(k,i)*eesij/fac_shield(i)*2.0
+ & grad_shield(k,i)*eesij/fac_shield(i)*2.0*sss
gshieldc(k,j-1)=gshieldc(k,j-1)+
- & grad_shield(k,j)*eesij/fac_shield(j)*2.0
+ & grad_shield(k,j)*eesij/fac_shield(j)*2.0*sss
enddo
endif
cgrad gelc(l,k)=gelc(l,k)+ggg(l)
cgrad enddo
cgrad enddo
- if (sss.gt.0.0) then
- ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
- ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
- ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
- else
- ggg(1)=0.0
- ggg(2)=0.0
- ggg(3)=0.0
- endif
+ facvdw=facvdw+sssgrad*rmij*evdwij
+ ggg(1)=facvdw*xj
+ ggg(2)=facvdw*yj
+ ggg(3)=facvdw*zj
c do k=1,3
c ghalf=0.5D0*ggg(k)
c gvdwpp(k,i)=gvdwpp(k,i)+ghalf
cgrad enddo
#else
C MARYSIA
- facvdw=(ev1+evdwij)*sss
+ facvdw=(ev1+evdwij)
facel=(el1+eesij)
fac1=fac
- fac=-3*rrmij*(facvdw+facvdw+facel)
+ fac=-3*rrmij*(facvdw+facvdw+facel)*sss
+ & +(evdwij+eesij)*sssgrad*rrmij
erij(1)=xj*rmij
erij(2)=yj*rmij
erij(3)=zj*rmij
do k=1,3
gelc(k,i)=gelc(k,i)
& +((ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
- & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1))
+ & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1))*sss
& *fac_shield(i)**2*fac_shield(j)**2
gelc(k,j)=gelc(k,j)
& +((ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
- & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1))
+ & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1))*sss
& *fac_shield(i)**2*fac_shield(j)**2
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
C fac_shield(j)=0.6
endif
eel_loc_ij=eel_loc_ij
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
c if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
c & 'eelloc',i,j,eel_loc_ij
C Now derivative over eel_loc
iresshield=shield_list(ilist,i)
do k=1,3
rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij
- & /fac_shield(i)
+ & /fac_shield(i)*sss
C & *2.0
gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
& rlocshield
- & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i)
+ & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i)*sss
gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
& +rlocshield
enddo
iresshield=shield_list(ilist,j)
do k=1,3
rlocshield=grad_shield_side(k,ilist,j)*eel_loc_ij
- & /fac_shield(j)
+ & /fac_shield(j)*sss
C & *2.0
gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
& rlocshield
- & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j)
+ & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j)*sss
gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
& +rlocshield
do k=1,3
gshieldc_ll(k,i)=gshieldc_ll(k,i)+
- & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)*sss
gshieldc_ll(k,j)=gshieldc_ll(k,j)+
- & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)*sss
gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+
- & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)*sss
gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+
- & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)*sss
enddo
endif
& +a23*gmuij1(2)
& +a32*gmuij1(3)
& +a33*gmuij1(4))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
c write(iout,*) "derivative over thatai"
c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
c & a33*gmuij1(4)
& +a33*gmuij2(4)
gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
& geel_loc_ij*wel_loc
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
c Derivative over j residue
geel_loc_ji=a22*gmuji1(1)
gloc(nphi+j,icg)=gloc(nphi+j,icg)+
& geel_loc_ji*wel_loc
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
geel_loc_ji=
& +a22*gmuji2(1)
c & a33*gmuji2(4)
gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+
& geel_loc_ji*wel_loc
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
& 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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
gel_loc_long(l,j)=gel_loc_long(l,j)+ggg(l)
gel_loc_long(l,i)=gel_loc_long(l,i)-ggg(l)
cgrad ghalf=0.5d0*ggg(l)
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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))
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
enddo
ENDIF
C Change 12/26/95 to calculate four-body contributions to H-bonding energy
c if (j.gt.i+1 .and. num_conti.le.maxconts) then
+#ifdef FOURBODY
if (wcorr+wcorr4+wcorr5+wcorr6.gt.0.0d0
& .and. num_conti.le.maxconts) then
c write (iout,*) i,j," entered corr"
C fac_shield(j)=0.6d0
endif
ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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
gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
enddo
gggp(1)=gggp(1)+ees0pijp*xj
+ & +ees0p(num_conti,i)/sss*rmij*xj*sssgrad
gggp(2)=gggp(2)+ees0pijp*yj
+ & +ees0p(num_conti,i)/sss*rmij*yj*sssgrad
gggp(3)=gggp(3)+ees0pijp*zj
+ & +ees0p(num_conti,i)/sss*rmij*zj*sssgrad
gggm(1)=gggm(1)+ees0mijp*xj
+ & +ees0m(num_conti,i)/sss*rmij*xj*sssgrad
gggm(2)=gggm(2)+ees0mijp*yj
+ & +ees0m(num_conti,i)/sss*rmij*yj*sssgrad
gggm(3)=gggm(3)+ees0mijp*zj
+ & +ees0m(num_conti,i)/sss*rmij*zj*sssgrad
C Derivatives due to the contact function
gacont_hbr(1,num_conti,i)=fprimcont*xj
gacont_hbr(2,num_conti,i)=fprimcont*yj
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)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
gacontp_hb3(k,num_conti,i)=gggp(k)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
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)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
gacontm_hb3(k,num_conti,i)=gggm(k)
- & *fac_shield(i)*fac_shield(j)
+ & *fac_shield(i)*fac_shield(j)*sss
enddo
C Diagnostics. Comment out or remove after debugging!
endif ! num_conti.le.maxconts
endif ! fcont.gt.0
endif ! j.gt.i+1
+#endif
if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
do k=1,4
do l=1,3
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
- include 'COMMON.CONTACTS'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
- include 'COMMON.CONTACTS'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
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)
+ implicit none
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.CONTROL'
include 'COMMON.SPLITELE'
integer xshift,yshift,zshift
- dimension ggg(3)
+ double precision ggg(3)
+ integer i,iint,j,k,iteli,itypj,subchap
+ double precision xi,yi,zi,xj,yj,zj,rrij,sss1,sssgrad1,
+ & fac,e1,e2,rij
+ double precision evdw2,evdw2_14,evdwij
+ double precision xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,
+ & dist_temp, dist_init
+ double precision sscale,sscagrad
evdw2=0.0D0
evdw2_14=0.0d0
c print *,boxxsize,boxysize,boxzsize,'wymiary pudla'
C do xshift=-1,1
C do yshift=-1,1
C do zshift=-1,1
- if (energy_dec) write (iout,*) "escp:",r_cut,rlamb
+ if (energy_dec) write (iout,*) "escp:",r_cut_int,rlamb
do i=iatscp_s,iatscp_e
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
c print *,xj,yj,zj,'polozenie j'
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
c print *,rrij
- sss=sscale(1.0d0/(dsqrt(rrij)))
+ sss=sscale(1.0d0/(dsqrt(rrij)),r_cut_int)
c print *,r_cut,1.0d0/dsqrt(rrij),sss,'tu patrz'
c if (sss.eq.0) print *,'czasem jest OK'
if (sss.le.0.0d0) cycle
- sssgrad=sscagrad(1.0d0/(dsqrt(rrij)))
+ sssgrad=sscagrad(1.0d0/(dsqrt(rrij)),r_cut_int)
fac=rrij**expon2
e1=fac*fac*aad(itypj,iteli)
e2=fac*bad(itypj,iteli)
endif
evdwij=e1+e2
evdw2=evdw2+evdwij*sss
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
- & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+ if (energy_dec) write (iout,'(a6,2i5,3f7.3,2i3,3e11.3)')
+ & 'evdw2',i,j,1.0d0/dsqrt(rrij),sss,
+ & evdwij,iteli,itypj,fac,aad(itypj,iteli),
& bad(itypj,iteli)
C
C Calculate contributions to the gradient in the virtual-bond and SC vectors.
estr=0.0d0
estr1=0.0d0
do i=ibondp_start,ibondp_end
+c 3/4/2020 Adam: removed dummy bond graient if Calpha and SC coords are
+c used
+#ifdef FIVEDIAG
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) cycle
+ diff = vbld(i)-vbldp0
+#else
if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle
c estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
c do j=1,3
c & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax)
c else
C Checking if it involves dummy (NH3+ or COO-) group
- if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
+ if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
C YES vbldpDUM is the equlibrium length of spring for Dummy atom
- diff = vbld(i)-vbldpDUM
- if (energy_dec) write(iout,*) "dum_bond",i,diff
- else
-C NO vbldp0 is the equlibrium lenght of spring for peptide group
- diff = vbld(i)-vbldp0
- endif
- if (energy_dec) write (iout,'(a7,i5,4f7.3)')
+ diff = vbld(i)-vbldpDUM
+ if (energy_dec) write(iout,*) "dum_bond",i,diff
+ else
+C NO vbldp0 is the equlibrium length of spring for peptide group
+ diff = vbld(i)-vbldp0
+ endif
+#endif
+ if (energy_dec) write (iout,'(a7,i5,4f7.3)')
& "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff
estr=estr+diff*diff
do j=1,3
c & dscp1,dscp2,sumene
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
-c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i)
+ if (energy_dec) write (2,*) "i",i," itype",itype(i)," it",it,
+ & " escloc",sumene,escloc,it,itype(i)
c & ,zz,xx,yy
c#define DEBUG
#ifdef DEBUG
return
end
c----------------------------------------------------------------------------
+c LICZENIE WIEZOW Z ROWNANIA ENERGII MODELLERA
+ subroutine e_modeller(ehomology_constr)
+ ehomology_constr=0.0d0
+ write (iout,*) "!!!!!UWAGA, JESTEM W DZIWNEJ PETLI, TEST!!!!!"
+ return
+ end
+C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
+
+c------------------------------------------------------------------------------
+ subroutine etor_d(etors_d)
+ etors_d=0.0d0
+ return
+ end
+c----------------------------------------------------------------------------
#else
subroutine etor(etors)
implicit real*8 (a-h,o-z)
return
end
c----------------------------------------------------------------------------
+c MODELLER restraint function
+ subroutine e_modeller(ehomology_constr)
+ implicit none
+ include 'DIMENSIONS'
+
+ double precision ehomology_constr
+ integer nnn,i,ii,j,k,ijk,jik,ki,kk,nexl,irec,l
+ integer katy, odleglosci, test7
+ real*8 odleg, odleg2, odleg3, kat, kat2, kat3, gdih(max_template)
+ real*8 Eval,Erot
+ real*8 distance(max_template),distancek(max_template),
+ & min_odl,godl(max_template),dih_diff(max_template)
+
+c
+c FP - 30/10/2014 Temporary specifications for homology restraints
+c
+ double precision utheta_i,gutheta_i,sum_gtheta,sum_sgtheta,
+ & sgtheta
+ double precision, dimension (maxres) :: guscdiff,usc_diff
+ double precision, dimension (max_template) ::
+ & gtheta,dscdiff,uscdiffk,guscdiff2,guscdiff3,
+ & theta_diff
+ double precision sum_godl,sgodl,grad_odl3,ggodl,sum_gdih,
+ & sum_guscdiff,sum_sgdih,sgdih,grad_dih3,usc_diff_i,dxx,dyy,dzz,
+ & betai,sum_sgodl,dij
+ double precision dist,pinorm
+c
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.CHAIN'
+ include 'COMMON.GEO'
+ include 'COMMON.DERIV'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.VAR'
+ include 'COMMON.IOUNITS'
+c include 'COMMON.MD'
+ include 'COMMON.CONTROL'
+ include 'COMMON.HOMOLOGY'
+ include 'COMMON.QRESTR'
+c
+c From subroutine Econstr_back
+c
+ include 'COMMON.NAMES'
+ include 'COMMON.TIME1'
+c
+
+
+ do i=1,max_template
+ distancek(i)=9999999.9
+ enddo
+
+
+ odleg=0.0d0
+
+c Pseudo-energy and gradient from homology restraints (MODELLER-like
+c function)
+C AL 5/2/14 - Introduce list of restraints
+c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+#ifdef DEBUG
+ write(iout,*) "------- dist restrs start -------"
+#endif
+ do ii = link_start_homo,link_end_homo
+ i = ires_homo(ii)
+ j = jres_homo(ii)
+ dij=dist(i,j)
+c write (iout,*) "dij(",i,j,") =",dij
+ nexl=0
+ do k=1,constr_homology
+c write(iout,*) ii,k,i,j,l_homo(k,ii),dij,odl(k,ii)
+ if(.not.l_homo(k,ii)) then
+ nexl=nexl+1
+ cycle
+ endif
+ distance(k)=odl(k,ii)-dij
+c write (iout,*) "distance(",k,") =",distance(k)
+c
+c For Gaussian-type Urestr
+c
+ distancek(k)=0.5d0*distance(k)**2*sigma_odl(k,ii) ! waga_dist rmvd from Gaussian argument
+c write (iout,*) "sigma_odl(",k,ii,") =",sigma_odl(k,ii)
+c write (iout,*) "distancek(",k,") =",distancek(k)
+c distancek(k)=0.5d0*waga_dist*distance(k)**2*sigma_odl(k,ii)
+c
+c For Lorentzian-type Urestr
+c
+ if (waga_dist.lt.0.0d0) then
+ sigma_odlir(k,ii)=dsqrt(1/sigma_odl(k,ii))
+ distancek(k)=distance(k)**2/(sigma_odlir(k,ii)*
+ & (distance(k)**2+sigma_odlir(k,ii)**2))
+ endif
+ enddo
+
+c min_odl=minval(distancek)
+ do kk=1,constr_homology
+ if(l_homo(kk,ii)) then
+ min_odl=distancek(kk)
+ exit
+ endif
+ enddo
+ do kk=1,constr_homology
+ if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
+ & min_odl=distancek(kk)
+ enddo
+
+c write (iout,* )"min_odl",min_odl
+#ifdef DEBUG
+ write (iout,*) "ij dij",i,j,dij
+ write (iout,*) "distance",(distance(k),k=1,constr_homology)
+ write (iout,*) "distancek",(distancek(k),k=1,constr_homology)
+ write (iout,* )"min_odl",min_odl
+#endif
+#ifdef OLDRESTR
+ odleg2=0.0d0
+#else
+ if (waga_dist.ge.0.0d0) then
+ odleg2=nexl
+ else
+ odleg2=0.0d0
+ endif
+#endif
+ do k=1,constr_homology
+c Nie wiem po co to liczycie jeszcze raz!
+c odleg3=-waga_dist(iset)*((distance(i,j,k)**2)/
+c & (2*(sigma_odl(i,j,k))**2))
+ if(.not.l_homo(k,ii)) cycle
+ if (waga_dist.ge.0.0d0) then
+c
+c For Gaussian-type Urestr
+c
+ godl(k)=dexp(-distancek(k)+min_odl)
+ odleg2=odleg2+godl(k)
+c
+c For Lorentzian-type Urestr
+c
+ else
+ odleg2=odleg2+distancek(k)
+ endif
+
+ccc write(iout,779) i,j,k, "odleg2=",odleg2, "odleg3=", odleg3,
+ccc & "dEXP(odleg3)=", dEXP(odleg3),"distance(i,j,k)^2=",
+ccc & distance(i,j,k)**2, "dist(i+1,j+1)=", dist(i+1,j+1),
+ccc & "sigma_odl(i,j,k)=", sigma_odl(i,j,k)
+
+ enddo
+c write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
+c write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
+#ifdef DEBUG
+ write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
+ write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
+#endif
+ if (waga_dist.ge.0.0d0) then
+c
+c For Gaussian-type Urestr
+c
+ odleg=odleg-dLOG(odleg2/constr_homology)+min_odl
+c
+c For Lorentzian-type Urestr
+c
+ else
+ odleg=odleg+odleg2/constr_homology
+ endif
+c
+c write (iout,*) "odleg",odleg ! sum of -ln-s
+c Gradient
+c
+c For Gaussian-type Urestr
+c
+ if (waga_dist.ge.0.0d0) sum_godl=odleg2
+ sum_sgodl=0.0d0
+ do k=1,constr_homology
+c godl=dexp(((-(distance(i,j,k)**2)/(2*(sigma_odl(i,j,k))**2))
+c & *waga_dist)+min_odl
+c sgodl=-godl(k)*distance(k)*sigma_odl(k,ii)*waga_dist
+c
+ if(.not.l_homo(k,ii)) cycle
+ if (waga_dist.ge.0.0d0) then
+c For Gaussian-type Urestr
+c
+ sgodl=-godl(k)*distance(k)*sigma_odl(k,ii) ! waga_dist rmvd
+c
+c For Lorentzian-type Urestr
+c
+ else
+ sgodl=-2*sigma_odlir(k,ii)*(distance(k)/(distance(k)**2+
+ & sigma_odlir(k,ii)**2)**2)
+ endif
+ sum_sgodl=sum_sgodl+sgodl
+
+c sgodl2=sgodl2+sgodl
+c write(iout,*) i, j, k, distance(i,j,k), "W GRADIENCIE1"
+c write(iout,*) "constr_homology=",constr_homology
+c write(iout,*) i, j, k, "TEST K"
+ enddo
+ if (waga_dist.ge.0.0d0) then
+c
+c For Gaussian-type Urestr
+c
+ grad_odl3=waga_homology(iset)*waga_dist
+ & *sum_sgodl/(sum_godl*dij)
+c
+c For Lorentzian-type Urestr
+c
+ else
+c Original grad expr modified by analogy w Gaussian-type Urestr grad
+c grad_odl3=-waga_homology(iset)*waga_dist*sum_sgodl
+ grad_odl3=-waga_homology(iset)*waga_dist*
+ & sum_sgodl/(constr_homology*dij)
+ endif
+c
+c grad_odl3=sum_sgodl/(sum_godl*dij)
+
+
+c write(iout,*) i, j, k, distance(i,j,k), "W GRADIENCIE2"
+c write(iout,*) (distance(i,j,k)**2), (2*(sigma_odl(i,j,k))**2),
+c & (-(distance(i,j,k)**2)/(2*(sigma_odl(i,j,k))**2))
+
+ccc write(iout,*) godl, sgodl, grad_odl3
+
+c grad_odl=grad_odl+grad_odl3
+
+ do jik=1,3
+ ggodl=grad_odl3*(c(jik,i)-c(jik,j))
+ccc write(iout,*) c(jik,i+1), c(jik,j+1), (c(jik,i+1)-c(jik,j+1))
+ccc write(iout,746) "GRAD_ODL_1", i, j, jik, ggodl,
+ccc & ghpbc(jik,i+1), ghpbc(jik,j+1)
+ ghpbc(jik,i)=ghpbc(jik,i)+ggodl
+ ghpbc(jik,j)=ghpbc(jik,j)-ggodl
+ccc write(iout,746) "GRAD_ODL_2", i, j, jik, ggodl,
+ccc & ghpbc(jik,i+1), ghpbc(jik,j+1)
+c if (i.eq.25.and.j.eq.27) then
+c write(iout,*) "jik",jik,"i",i,"j",j
+c write(iout,*) "sum_sgodl",sum_sgodl,"sgodl",sgodl
+c write(iout,*) "grad_odl3",grad_odl3
+c write(iout,*) "c(",jik,i,")",c(jik,i),"c(",jik,j,")",c(jik,j)
+c write(iout,*) "ggodl",ggodl
+c write(iout,*) "ghpbc(",jik,i,")",
+c & ghpbc(jik,i),"ghpbc(",jik,j,")",
+c & ghpbc(jik,j)
+c endif
+ enddo
+ccc write(iout,778)"TEST: odleg2=", odleg2, "DLOG(odleg2)=",
+ccc & dLOG(odleg2),"-odleg=", -odleg
+
+ enddo ! ii-loop for dist
+#ifdef DEBUG
+ write(iout,*) "------- dist restrs end -------"
+c if (waga_angle.eq.1.0d0 .or. waga_theta.eq.1.0d0 .or.
+c & waga_d.eq.1.0d0) call sum_gradient
+#endif
+c Pseudo-energy and gradient from dihedral-angle restraints from
+c homology templates
+c write (iout,*) "End of distance loop"
+c call flush(iout)
+ kat=0.0d0
+c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
+#ifdef DEBUG
+ write(iout,*) "------- dih restrs start -------"
+ do i=idihconstr_start_homo,idihconstr_end_homo
+ write (iout,*) "gloc_init(",i,icg,")",gloc(i,icg)
+ enddo
+#endif
+ do i=idihconstr_start_homo,idihconstr_end_homo
+ kat2=0.0d0
+c betai=beta(i,i+1,i+2,i+3)
+ betai = phi(i)
+c write (iout,*) "betai =",betai
+ do k=1,constr_homology
+ dih_diff(k)=pinorm(dih(k,i)-betai)
+cd write (iout,'(a8,2i4,2f15.8)') "dih_diff",i,k,dih_diff(k)
+cd & ,sigma_dih(k,i)
+c if (dih_diff(i,k).gt.3.14159) dih_diff(i,k)=
+c & -(6.28318-dih_diff(i,k))
+c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
+c & 6.28318+dih_diff(i,k)
+#ifdef OLD_DIHED
+ kat3=-0.5d0*dih_diff(k)**2*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
+#else
+ kat3=(dcos(dih_diff(k))-1)*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
+#endif
+c kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
+ gdih(k)=dexp(kat3)
+ kat2=kat2+gdih(k)
+c write(iout,*) "kat2=", kat2, "exp(kat3)=", exp(kat3)
+c write(*,*)""
+ enddo
+c write (iout,*) "gdih",(gdih(k),k=1,constr_homology) ! exps
+c write (iout,*) "i",i," betai",betai," kat2",kat2 ! sum of exps
+#ifdef DEBUG
+ write (iout,*) "i",i," betai",betai," kat2",kat2
+ write (iout,*) "gdih",(gdih(k),k=1,constr_homology)
+#endif
+ if (kat2.le.1.0d-14) cycle
+ kat=kat-dLOG(kat2/constr_homology)
+c write (iout,*) "kat",kat ! sum of -ln-s
+
+ccc write(iout,778)"TEST: kat2=", kat2, "DLOG(kat2)=",
+ccc & dLOG(kat2), "-kat=", -kat
+
+c ----------------------------------------------------------------------
+c Gradient
+c ----------------------------------------------------------------------
+
+ sum_gdih=kat2
+ sum_sgdih=0.0d0
+ do k=1,constr_homology
+#ifdef OLD_DIHED
+ sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i) ! waga_angle rmvd
+#else
+ sgdih=-gdih(k)*dsin(dih_diff(k))*sigma_dih(k,i) ! waga_angle rmvd
+#endif
+c sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
+ sum_sgdih=sum_sgdih+sgdih
+ enddo
+c grad_dih3=sum_sgdih/sum_gdih
+ grad_dih3=waga_homology(iset)*waga_angle*sum_sgdih/sum_gdih
+
+c write(iout,*)i,k,gdih,sgdih,beta(i+1,i+2,i+3,i+4),grad_dih3
+ccc write(iout,747) "GRAD_KAT_1", i, nphi, icg, grad_dih3,
+ccc & gloc(nphi+i-3,icg)
+ gloc(i-3,icg)=gloc(i-3,icg)+grad_dih3
+c if (i.eq.25) then
+c write(iout,*) "i",i,"icg",icg,"gloc(",i,icg,")",gloc(i,icg)
+c endif
+ccc write(iout,747) "GRAD_KAT_2", i, nphi, icg, grad_dih3,
+ccc & gloc(nphi+i-3,icg)
+
+ enddo ! i-loop for dih
+#ifdef DEBUG
+ write(iout,*) "------- dih restrs end -------"
+#endif
+
+c Pseudo-energy and gradient for theta angle restraints from
+c homology templates
+c FP 01/15 - inserted from econstr_local_test.F, loop structure
+c adapted
+
+c
+c For constr_homology reference structures (FP)
+c
+c Uconst_back_tot=0.0d0
+ Eval=0.0d0
+ Erot=0.0d0
+c Econstr_back legacy
+ do i=1,nres
+c do i=ithet_start,ithet_end
+ dutheta(i)=0.0d0
+c enddo
+c do i=loc_start,loc_end
+ do j=1,3
+ duscdiff(j,i)=0.0d0
+ duscdiffx(j,i)=0.0d0
+ enddo
+ enddo
+c
+c do iref=1,nref
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "waga_theta",waga_theta
+ if (waga_theta.gt.0.0d0) then
+#ifdef DEBUG
+ write (iout,*) "usampl",usampl
+ write(iout,*) "------- theta restrs start -------"
+c do i=ithet_start,ithet_end
+c write (iout,*) "gloc_init(",nphi+i,icg,")",gloc(nphi+i,icg)
+c enddo
+#endif
+c write (iout,*) "maxres",maxres,"nres",nres
+
+ do i=ithet_start,ithet_end
+c
+c do i=1,nfrag_back
+c ii = ifrag_back(2,i,iset)-ifrag_back(1,i,iset)
+c
+c Deviation of theta angles wrt constr_homology ref structures
+c
+ utheta_i=0.0d0 ! argument of Gaussian for single k
+ gutheta_i=0.0d0 ! Sum of Gaussians over constr_homology ref structures
+c do j=ifrag_back(1,i,iset)+2,ifrag_back(2,i,iset) ! original loop
+c over residues in a fragment
+c write (iout,*) "theta(",i,")=",theta(i)
+ do k=1,constr_homology
+c
+c dtheta_i=theta(j)-thetaref(j,iref)
+c dtheta_i=thetaref(k,i)-theta(i) ! original form without indexing
+ theta_diff(k)=thetatpl(k,i)-theta(i)
+cd write (iout,'(a8,2i4,2f15.8)') "theta_diff",i,k,theta_diff(k)
+cd & ,sigma_theta(k,i)
+
+c
+ utheta_i=-0.5d0*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta rmvd from Gaussian argument
+c utheta_i=-0.5d0*waga_theta*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta?
+ gtheta(k)=dexp(utheta_i) ! + min_utheta_i?
+ gutheta_i=gutheta_i+gtheta(k) ! Sum of Gaussians (pk)
+c Gradient for single Gaussian restraint in subr Econstr_back
+c dutheta(j-2)=dutheta(j-2)+wfrag_back(1,i,iset)*dtheta_i/(ii-1)
+c
+ enddo
+c write (iout,*) "gtheta",(gtheta(k),k=1,constr_homology) ! exps
+c write (iout,*) "i",i," gutheta_i",gutheta_i ! sum of exps
+
+c
+c Gradient for multiple Gaussian restraint
+ sum_gtheta=gutheta_i
+ sum_sgtheta=0.0d0
+ do k=1,constr_homology
+c New generalized expr for multiple Gaussian from Econstr_back
+ sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i) ! waga_theta rmvd
+c
+c sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i)*waga_theta ! right functional form?
+ sum_sgtheta=sum_sgtheta+sgtheta ! cum variable
+ enddo
+c Final value of gradient using same var as in Econstr_back
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)
+ & +sum_sgtheta/sum_gtheta*waga_theta
+ & *waga_homology(iset)
+c dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
+c & *waga_homology(iset)
+c dutheta(i)=sum_sgtheta/sum_gtheta
+c
+c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
+ Eval=Eval-dLOG(gutheta_i/constr_homology)
+c write (iout,*) "utheta(",i,")=",utheta(i) ! -ln of sum of exps
+c write (iout,*) "Uconst_back",Uconst_back ! sum of -ln-s
+c Uconst_back=Uconst_back+utheta(i)
+ enddo ! (i-loop for theta)
+#ifdef DEBUG
+ write(iout,*) "------- theta restrs end -------"
+#endif
+ endif
+c
+c Deviation of local SC geometry
+c
+c Separation of two i-loops (instructed by AL - 11/3/2014)
+c
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c write (iout,*) "waga_d",waga_d
+
+#ifdef DEBUG
+ write(iout,*) "------- SC restrs start -------"
+ write (iout,*) "Initial duscdiff,duscdiffx"
+ do i=loc_start,loc_end
+ write (iout,*) i,(duscdiff(jik,i),jik=1,3),
+ & (duscdiffx(jik,i),jik=1,3)
+ enddo
+#endif
+ do i=loc_start,loc_end
+ usc_diff_i=0.0d0 ! argument of Gaussian for single k
+ guscdiff(i)=0.0d0 ! Sum of Gaussians over constr_homology ref structures
+c do j=ifrag_back(1,i,iset)+1,ifrag_back(2,i,iset)-1 ! Econstr_back legacy
+c write(iout,*) "xxtab, yytab, zztab"
+c write(iout,'(i5,3f8.2)') i,xxtab(i),yytab(i),zztab(i)
+ do k=1,constr_homology
+c
+ dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
+c Original sign inverted for calc of gradients (s. Econstr_back)
+ dyy=-yytpl(k,i)+yytab(i) ! ibid y
+ dzz=-zztpl(k,i)+zztab(i) ! ibid z
+c write(iout,*) "dxx, dyy, dzz"
+cd write(iout,'(2i5,4f8.2)') k,i,dxx,dyy,dzz,sigma_d(k,i)
+c
+ usc_diff_i=-0.5d0*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d rmvd from Gaussian argument
+c usc_diff(i)=-0.5d0*waga_d*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d?
+c uscdiffk(k)=usc_diff(i)
+ guscdiff2(k)=dexp(usc_diff_i) ! without min_scdiff
+c write(iout,*) "i",i," k",k," sigma_d",sigma_d(k,i),
+c & " guscdiff2",guscdiff2(k)
+ guscdiff(i)=guscdiff(i)+guscdiff2(k) !Sum of Gaussians (pk)
+c write (iout,'(i5,6f10.5)') j,xxtab(j),yytab(j),zztab(j),
+c & xxref(j),yyref(j),zzref(j)
+ enddo
+c
+c Gradient
+c
+c Generalized expression for multiple Gaussian acc to that for a single
+c Gaussian in Econstr_back as instructed by AL (FP - 03/11/2014)
+c
+c Original implementation
+c sum_guscdiff=guscdiff(i)
+c
+c sum_sguscdiff=0.0d0
+c do k=1,constr_homology
+c sguscdiff=-guscdiff2(k)*dscdiff(k)*sigma_d(k,i)*waga_d !waga_d?
+c sguscdiff=-guscdiff3(k)*dscdiff(k)*sigma_d(k,i)*waga_d ! w min_uscdiff
+c sum_sguscdiff=sum_sguscdiff+sguscdiff
+c enddo
+c
+c Implementation of new expressions for gradient (Jan. 2015)
+c
+c grad_uscdiff=sum_sguscdiff/(sum_guscdiff*dtab) !?
+ do k=1,constr_homology
+c
+c New calculation of dxx, dyy, and dzz corrected by AL (07/11), was missing and wrong
+c before. Now the drivatives should be correct
+c
+ dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
+c Original sign inverted for calc of gradients (s. Econstr_back)
+ dyy=-yytpl(k,i)+yytab(i) ! ibid y
+ dzz=-zztpl(k,i)+zztab(i) ! ibid z
+c
+c New implementation
+c
+ sum_guscdiff=guscdiff2(k)*!(dsqrt(dxx*dxx+dyy*dyy+dzz*dzz))* -> wrong!
+ & sigma_d(k,i) ! for the grad wrt r'
+c sum_sguscdiff=sum_sguscdiff+sum_guscdiff
+c
+c
+c New implementation
+ sum_guscdiff = waga_homology(iset)*waga_d*sum_guscdiff
+ do jik=1,3
+ duscdiff(jik,i-1)=duscdiff(jik,i-1)+
+ & sum_guscdiff*(dXX_C1tab(jik,i)*dxx+
+ & dYY_C1tab(jik,i)*dyy+dZZ_C1tab(jik,i)*dzz)/guscdiff(i)
+ duscdiff(jik,i)=duscdiff(jik,i)+
+ & sum_guscdiff*(dXX_Ctab(jik,i)*dxx+
+ & dYY_Ctab(jik,i)*dyy+dZZ_Ctab(jik,i)*dzz)/guscdiff(i)
+ duscdiffx(jik,i)=duscdiffx(jik,i)+
+ & sum_guscdiff*(dXX_XYZtab(jik,i)*dxx+
+ & dYY_XYZtab(jik,i)*dyy+dZZ_XYZtab(jik,i)*dzz)/guscdiff(i)
+c
+#ifdef DEBUG
+ write(iout,*) "jik",jik,"i",i
+ write(iout,*) "dxx, dyy, dzz"
+ write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
+ write(iout,*) "guscdiff2(",k,")",guscdiff2(k)
+c write(iout,*) "sum_sguscdiff",sum_sguscdiff
+cc write(iout,*) "dXX_Ctab(",jik,i,")",dXX_Ctab(jik,i)
+c write(iout,*) "dYY_Ctab(",jik,i,")",dYY_Ctab(jik,i)
+c write(iout,*) "dZZ_Ctab(",jik,i,")",dZZ_Ctab(jik,i)
+c write(iout,*) "dXX_C1tab(",jik,i,")",dXX_C1tab(jik,i)
+c write(iout,*) "dYY_C1tab(",jik,i,")",dYY_C1tab(jik,i)
+c write(iout,*) "dZZ_C1tab(",jik,i,")",dZZ_C1tab(jik,i)
+c write(iout,*) "dXX_XYZtab(",jik,i,")",dXX_XYZtab(jik,i)
+c write(iout,*) "dYY_XYZtab(",jik,i,")",dYY_XYZtab(jik,i)
+c write(iout,*) "dZZ_XYZtab(",jik,i,")",dZZ_XYZtab(jik,i)
+c write(iout,*) "duscdiff(",jik,i-1,")",duscdiff(jik,i-1)
+c write(iout,*) "duscdiff(",jik,i,")",duscdiff(jik,i)
+c write(iout,*) "duscdiffx(",jik,i,")",duscdiffx(jik,i)
+c endif
+#endif
+ enddo
+ enddo
+c
+c uscdiff(i)=-dLOG(guscdiff(i)/(ii-1)) ! Weighting by (ii-1) required?
+c usc_diff(i)=-dLOG(guscdiff(i)/constr_homology) ! + min_uscdiff ?
+c
+c write (iout,*) i," uscdiff",uscdiff(i)
+c
+c Put together deviations from local geometry
+
+c Uconst_back=Uconst_back+wfrag_back(1,i,iset)*utheta(i)+
+c & wfrag_back(3,i,iset)*uscdiff(i)
+ Erot=Erot-dLOG(guscdiff(i)/constr_homology)
+c write (iout,*) "usc_diff(",i,")=",usc_diff(i) ! -ln of sum of exps
+c write (iout,*) "Uconst_back",Uconst_back ! cum sum of -ln-s
+c Uconst_back=Uconst_back+usc_diff(i)
+c
+c Gradient of multiple Gaussian restraint (FP - 04/11/2014 - right?)
+c
+c New implment: multiplied by sum_sguscdiff
+c
+
+ enddo ! (i-loop for dscdiff)
+
+c endif
+
+#ifdef DEBUG
+ write(iout,*) "------- SC restrs end -------"
+ write (iout,*) "------ After SC loop in e_modeller ------"
+ do i=loc_start,loc_end
+ write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
+ write (iout,*) "i",i," gradx",(gradx(j,i,icg),j=1,3)
+ enddo
+ if (waga_theta.eq.1.0d0) then
+ write (iout,*) "in e_modeller after SC restr end: dutheta"
+ do i=ithet_start,ithet_end
+ write (iout,*) i,dutheta(i)
+ enddo
+ endif
+ if (waga_d.eq.1.0d0) then
+ write (iout,*) "e_modeller after SC loop: duscdiff/x"
+ do i=1,nres
+ write (iout,*) i,(duscdiff(j,i),j=1,3)
+ write (iout,*) i,(duscdiffx(j,i),j=1,3)
+ enddo
+ endif
+#endif
+
+c Total energy from homology restraints
+#ifdef DEBUG
+ write (iout,*) "odleg",odleg," kat",kat
+#endif
+c
+c Addition of energy of theta angle and SC local geom over constr_homologs ref strs
+c
+c ehomology_constr=odleg+kat
+c
+c For Lorentzian-type Urestr
+c
+
+ if (waga_dist.ge.0.0d0) then
+c
+c For Gaussian-type Urestr
+c
+ ehomology_constr=(waga_dist*odleg+waga_angle*kat+
+ & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
+c write (iout,*) "ehomology_constr=",ehomology_constr
+ else
+c
+c For Lorentzian-type Urestr
+c
+ ehomology_constr=(-waga_dist*odleg+waga_angle*kat+
+ & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
+c write (iout,*) "ehomology_constr=",ehomology_constr
+ endif
+#ifdef DEBUG
+ write (iout,*) "odleg",waga_dist,odleg," kat",waga_angle,kat,
+ & "Eval",waga_theta,eval,
+ & "Erot",waga_d,Erot
+ write (iout,*) "ehomology_constr",ehomology_constr
+#endif
+ return
+c
+c FP 01/15 end
+c
+ 748 format(a8,f12.3,a6,f12.3,a7,f12.3)
+ 747 format(a12,i4,i4,i4,f8.3,f8.3)
+ 746 format(a12,i4,i4,i4,f8.3,f8.3,f8.3)
+ 778 format(a7,1X,f10.3,1X,a4,1X,f10.3,1X,a5,1X,f10.3)
+ 779 format(i3,1X,i3,1X,i2,1X,a7,1X,f7.3,1X,a7,1X,f7.3,1X,a13,1X,
+ & f7.3,1X,a17,1X,f9.3,1X,a10,1X,f8.3,1X,a10,1X,f8.3)
+ end
+c----------------------------------------------------------------------------
C The rigorous attempt to derive energy function
subroutine ebend_kcc(etheta)
return
end
+#ifdef FOURBODY
c----------------------------------------------------------------------------
subroutine multibody(ecorr)
C This subroutine calculates multi-body contributions to energy following
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
double precision gx(3),gx1(3)
logical lprn
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
logical lprn
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.CONTROL'
include 'COMMON.LOCAL'
double precision gx(3),gx1(3),time00
parameter (max_cont=maxconts)
parameter (max_dim=26)
include "COMMON.CONTACTS"
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
double precision zapas(max_dim,maxconts,max_fg_procs),
& zapas_recv(max_dim,maxconts,max_fg_procs)
common /przechowalnia/ zapas
include 'COMMON.LOCAL'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.CHAIN'
include 'COMMON.CONTROL'
include 'COMMON.SHIELD'
parameter (max_cont=maxconts)
parameter (max_dim=70)
include "COMMON.CONTACTS"
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
double precision zapas(max_dim,maxconts,max_fg_procs),
& zapas_recv(max_dim,maxconts,max_fg_procs)
common /przechowalnia/ zapas
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.SHIELD'
include 'COMMON.CONTROL'
double precision gx(3),gx1(3)
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTMAT'
+ include 'COMMON.CORRMAT'
include 'COMMON.TORSION'
include 'COMMON.VAR'
include 'COMMON.GEO'
cd write (2,*) 'eel_turn6',ekont*eel_turn6
return
end
-
C-----------------------------------------------------------------------------
+#endif
double precision function scalar(u,v)
!DIR$ INLINEALWAYS scalar
#ifndef OSF
include 'COMMON.INTERACT'
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
- include 'COMMON.MD'
+c include 'COMMON.MD'
+#ifdef LANG0
+#ifdef FIVEDIAG
+ include 'COMMON.LANGEVIN.lang0.5diag'
+#else
+ include 'COMMON.LANGEVIN.lang0'
+#endif
+#else
+ include 'COMMON.LANGEVIN'
+#endif
include 'COMMON.CONTROL'
+ include 'COMMON.SAXS'
include 'COMMON.NAMES'
include 'COMMON.TIME1'
include 'COMMON.FFIELD'
include 'COMMON.INTERACT'
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
- include 'COMMON.MD'
+c include 'COMMON.MD'
+#ifdef LANG0
+#ifdef FIVEDIAG
+ include 'COMMON.LANGEVIN.lang0.5diag'
+#else
+ include 'COMMON.LANGEVIN.lang0'
+#endif
+#else
+ include 'COMMON.LANGEVIN'
+#endif
include 'COMMON.CONTROL'
+ include 'COMMON.SAXS'
include 'COMMON.NAMES'
include 'COMMON.TIME1'
include 'COMMON.FFIELD'
projects / unres.git / blobdiff