From: Cezary Czaplewski Date: Sun, 17 Feb 2013 02:19:35 +0000 (+0100) Subject: Merge branch 'prerelease-3.2.1' into czarek X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=3176770f951fd8b689c14df6260e55fa4f479689;hp=-c;p=unres.git Merge branch 'prerelease-3.2.1' into czarek Conflicts: bin/unres/MD/unres_ifort_MPICH_GAB.exe source/unres/src_MD/cinfo.f source/unres/src_MD/energy_p_new_barrier.F --- 3176770f951fd8b689c14df6260e55fa4f479689 diff --combined bin/unres/MD/unres_ifort_MPICH_GAB.exe index 97d45b7,a5decdb..968912a Binary files differ diff --combined source/unres/src_MD/cinfo.f index 3f50f77,7534dcb..07a66c9 --- a/source/unres/src_MD/cinfo.f +++ b/source/unres/src_MD/cinfo.f @@@ -1,10 -1,10 +1,10 @@@ C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C - C 3 1 52 -C 3 1 78 ++C 3 1 53 subroutine cinfo include 'COMMON.IOUNITS' write(iout,*)'++++ Compile info ++++' - write(iout,*)'Version 3.1 build 52' - write(iout,*)'compiled Sun Feb 17 00:55:22 2013' - write(iout,*)'Version 3.1 build 78' - write(iout,*)'compiled Sun Feb 17 03:00:27 2013' ++ write(iout,*)'Version 3.1 build 53' ++ write(iout,*)'compiled Sun Feb 17 03:17:55 2013' write(iout,*)'compiled by czarek@piasek3' write(iout,*)'OS name: Linux ' write(iout,*)'OS release: 2.6.32-42-generic ' diff --combined source/unres/src_MD/energy_p_new_barrier.F index 102862a,64dd328..0af23e5 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@@ -428,14 -428,14 +428,14 @@@ cMS$ATTRIBUTES C :: proc_pro #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor @@@ -1057,25 -1057,25 +1057,25 @@@ C-------------------------------------- & edihcnstr,ebr*nss, & Uconst,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)'/ - & 'EHPB= ',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)'/ + & 'EHPB= ',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)'/ + & 'ECORR4=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR5=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & 'ECORR6=',1pE16.6,' WEIGHT=',1pE16.6,' (multi-body)'/ + & '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)'/ + & 'ETURN6=',1pE16.6,' WEIGHT=',1pE16.6,' (turns, 6th order)'/ + & 'ESCCOR=',1pE16.6,' WEIGHT=',1pE16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ @@@ -4257,8 -4257,8 +4257,8 @@@ 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 +c write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr +c 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 @@@ -4279,13 -4279,14 +4279,13 @@@ C 24/11/03 AL: SS bridges handled separ C distance and angle dependent SS bond potential. cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds - c if (.not.dyn_ss .and. i.le.nss) then - C 15/02/13 CC dynamic SSbond - if (.not.dyn_ss.and. - & ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then + if (.not.dyn_ss .and. i.le.nss) then + C 15/02/13 CC dynamic SSbond - additional check + 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 - c write (iout,*) "eij",eij + endif -cd write (iout,*) "eij",eij else if (ii.gt.nres .and. jj.gt.nres) then c Restraints from contact prediction dd=dist(ii,jj) @@@ -4423,9 -4424,8 +4423,9 @@@ c dscj_inv=dsc_inv(itypj deltat12=om2-om1+2.0d0 cosphi=om12-om1*om2 eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2) - & +akct*deltad*deltat12 + & +akct*deltad*deltat12+ebr & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi + & +ss_depth 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 diff --combined source/unres/src_MD/geomout.F index 8357bdb,0a46b14..09eb76e --- a/source/unres/src_MD/geomout.F +++ b/source/unres/src_MD/geomout.F @@@ -79,9 -79,15 +79,15 @@@ cmodel write (iunit,'(a5,i6)') 'MO if (nss.gt.0) then do i=1,nss + if (dyn_ss) then write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') - & 'SSBOND',i,'CYS',ihpb(i)-1-nres, - & 'CYS',jhpb(i)-1-nres + & 'SSBOND',i,'CYS',idssb(i)-nnt+1, + & 'CYS',jdssb(i)-nnt+1 + else + write(iunit,'(a6,i4,1x,a3,i7,4x,a3,i7)') + & 'SSBOND',i,'CYS',ihpb(i)-nnt+1-nres, + & 'CYS',jhpb(i)-nnt+1-nres + endif enddo endif @@@ -110,8 -116,11 +116,11 @@@ write (iunit,30) ica(nct),ica(nct)+1 endif do i=1,nss - c trzeba uporzdkowac - c write (iunit,30) ica(ihpb(i))+1,ica(jhpb(i))+1 + if (dyn_ss) then + write (iunit,30) ica(idssb(i))+1,ica(jdssb(i))+1 + else + write (iunit,30) ica(ihpb(i)-nres)+1,ica(jhpb(i)-nres)+1 + endif enddo write (iunit,'(a6)') 'ENDMDL' 10 FORMAT ('ATOM',I7,' CA ',A3,I6,4X,3F8.3,f15.3) @@@ -370,124 -379,6 +379,124 @@@ c-------------------------------------- #endif return end +c----------------------------------------------- + subroutine read_cx(ixdrf,*) +c xdrfopen should be called before this subroutine + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' +#ifdef MPI + include 'mpif.h' + include 'COMMON.SETUP' +#else + parameter (me=0) +#endif + include 'COMMON.CHAIN' + include 'COMMON.INTERACT' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.HEADER' + include 'COMMON.SBRIDGE' + include 'COMMON.DISTFIT' + include 'COMMON.MD' + include 'COMMON.LOCAL' + double precision time + integer iret,itmp + real xcoord(3,maxres2+2),prec + real r_time,r_potE,r_uconst,r_uconst_back,r_t_bath + + +#ifdef AIX +c call xdrfopen_(ixdrf,cartname, "r", iret) + call xdrffloat_(ixdrf, r_time, iret) + if(iret.eq.0) return1 + + call xdrffloat_(ixdrf, r_potE), iret) + call xdrffloat_(ixdrf, r_uconst), iret) + call xdrffloat_(ixdrf, r_uconst_back), iret) + call xdrffloat_(ixdrf, r_t_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, nfrag+npair+3*nfrag_back, iret) + do i=1,nfrag + call xdrffloat_(ixdrf, real(qfrag(i)), iret) + enddo + do i=1,npair + call xdrffloat_(ixdrf, real(qpair(i)), iret) + enddo + do i=1,nfrag_back + call xdrffloat_(ixdrf, real(utheta(i)), iret) + call xdrffloat_(ixdrf, real(ugamma(i)), iret) + call xdrffloat_(ixdrf, real(uscdiff(i)), iret) + enddo +#else +c call xdrfopen(ixdrf,cartname, "r", iret) + call xdrffloat(ixdrf, r_time, iret) + if(iret.eq.0) return1 + + call xdrffloat(ixdrf, r_potE, iret) + call xdrffloat(ixdrf, r_uconst, iret) + call xdrffloat(ixdrf, r_uconst_back, iret) + call xdrffloat(ixdrf, r_t_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, nfrag+npair+3*nfrag_back, iret) + do i=1,nfrag + call xdrffloat(ixdrf, real(qfrag(i)), iret) + enddo + do i=1,npair + call xdrffloat(ixdrf, real(qpair(i)), iret) + enddo + do i=1,nfrag_back + call xdrffloat(ixdrf, real(utheta(i)), iret) + call xdrffloat(ixdrf, real(ugamma(i)), iret) + call xdrffloat(ixdrf, real(uscdiff(i)), iret) + enddo +#endif + prec=10000.0 + + itmp=nres+nct-nnt+1 +#ifdef AIX + call xdrf3dfcoord_(ixdrf, xcoord, itmp, prec, iret) +c call xdrfclose_(ixdrf, iret) +#else + call xdrf3dfcoord(ixdrf, xcoord, itmp, prec, iret) +c call xdrfclose(ixdrf, iret) +#endif + + do i=1,nres + do j=1,3 + c(j,i)=xcoord(j,i) + enddo + enddo + do i=nnt,nct + do j=1,3 + c(j,i+nres)=xcoord(j,nres+i-nnt+1) + enddo + enddo + + call int_from_cart1(.false.) + + 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=2,nres-1 + 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 + + return + end #endif c----------------------------------------------------------------- subroutine statout(itime) diff --combined source/unres/src_MD/readrtns.F index a11f4fb,c5dc889..10cde78 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@@ -1127,8 -1127,8 +1127,8 @@@ czscore call geom_to_var(nvar, c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup if (constr_dist.gt.0) then call read_dist_constr - call hpb_partition endif + if (nhpb.gt.0) call hpb_partition c write (iout,*) "After read_dist_constr nhpb",nhpb c call flush(iout) if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 @@@ -1340,10 -1340,12 +1340,12 @@@ C Check whether the specified bridging do i=1,ns if (itype(iss(i)).ne.1) then if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, + & 'Do you REALLY think that the residue ', + & restyp(itype(iss(i))),i, & ' can form a disulfide bridge?!!!' write (*,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, + & 'Do you REALLY think that the residue ', + & restyp(itype(iss(i))),i, & ' can form a disulfide bridge?!!!' #ifdef MPI call MPI_Finalize(MPI_COMM_WORLD,ierror)