X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Fenergy_p_new_barrier.F;h=5ae5a4334d05b0046be933b8acb28f2b1759c0c6;hb=83bfd1e75fe4d7f79f4ec4b52f17743cb16a1fb2;hp=1692c50fdb7378c88541ef45181b074372d0a051;hpb=599d009baac6b0c6e8fad32a26767695425130e5;p=unres.git diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 1692c50..5ae5a43 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -131,6 +131,11 @@ C C Calculate electrostatic (H-bonding) energy of the main chain. C 107 continue +cmc +cmc Sep-06: egb takes care of dynamic ss bonds too +cmc +c if (dyn_ss) call dyn_set_nss + c print *,"Processor",myrank," computed USCSC" #ifdef TIMING #ifdef MPI @@ -326,6 +331,7 @@ C energia(23)=evdw_m c print *," Processor",myrank," calls SUM_ENERGY" call sum_energy(energia,.true.) + if (dyn_ss) call dyn_set_nss c print *," Processor",myrank," left SUM_ENERGY" #ifdef TIMING #ifdef MPI @@ -423,14 +429,14 @@ cMS$ATTRIBUTES C :: proc_proc #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*ecorr+wcorr5*ecorr5 + & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & +wbond*estr+Uconst+wsccor*esccor @@ -471,7 +477,7 @@ cMS$ATTRIBUTES C :: proc_proc include 'mpif.h' #endif double precision gradbufc(3,maxres),gradbufx(3,maxres), - & glocbuf(4*maxres),gradbufc_sum(3,maxres) + & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres) include 'COMMON.SETUP' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' @@ -483,6 +489,7 @@ cMS$ATTRIBUTES C :: proc_proc include 'COMMON.CONTROL' include 'COMMON.TIME1' include 'COMMON.MAXGRAD' + include 'COMMON.SCCOR' #ifdef TIMING #ifdef MPI time01=MPI_Wtime() @@ -755,7 +762,6 @@ c enddo & +wturn3*gel_loc_turn3(i) & +wturn6*gel_loc_turn6(i) & +wel_loc*gel_loc_loc(i) - & +wsccor*gsccor_loc(i) enddo #ifdef DEBUG write (iout,*) "gloc after adding corr" @@ -774,6 +780,19 @@ c enddo do i=1,4*nres glocbuf(i)=gloc(i,icg) enddo +#ifdef DEBUG + write (iout,*) "gloc_sc before reduce" + do i=1,nres + do j=1,3 + write (iout,*) i,j,gloc_sc(j,i,icg) + enddo + enddo +#endif + do i=1,nres + do j=1,3 + gloc_scbuf(j,i)=gloc_sc(j,i,icg) + enddo + enddo time00=MPI_Wtime() call MPI_Barrier(FG_COMM,IERR) time_barrier_g=time_barrier_g+MPI_Wtime()-time00 @@ -784,8 +803,18 @@ c enddo & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres, & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) time_reduce=time_reduce+MPI_Wtime()-time00 #ifdef DEBUG + write (iout,*) "gloc_sc after reduce" + do i=1,nres + do j=1,3 + write (iout,*) i,j,gloc_sc(j,i,icg) + enddo + enddo +#endif +#ifdef DEBUG write (iout,*) "gloc after reduce" do i=1,4*nres write (iout,*) i,gloc(i,icg) @@ -1029,25 +1058,25 @@ 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)'/ - & '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)'/ + & '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)'/ @@ -1529,6 +1558,7 @@ C include 'COMMON.IOUNITS' include 'COMMON.CALC' include 'COMMON.CONTROL' + include 'COMMON.SBRIDGE' logical lprn evdw=0.0D0 ccccc energy_dec=.false. @@ -1557,6 +1587,12 @@ C Calculate SC interaction energy. C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) + IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN + call dyn_ssbond_ene(i,j,evdwij) + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + & 'evdw',i,j,evdwij,' ss' + ELSE ind=ind+1 itypj=itype(j) c dscj_inv=dsc_inv(itypj) @@ -1666,6 +1702,7 @@ C Calculate angular part of the gradient. #else call sc_grad #endif + ENDIF ! dyn_ss enddo ! j enddo ! iint enddo ! i @@ -4239,49 +4276,96 @@ C iii and jjj point to the residues for which the distance is assigned. iii=ii jjj=jj endif -cd write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj +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 +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 + 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 + 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) + 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) - rdis=dd-dhpb(i) + 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) + waga=forcon(i) C Calculate the contribution to energy. - ehpb=ehpb+waga*rdis*rdis + ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "alpha reg",dd,waga*rdis*rdis C C Evaluate gradient. C - fac=waga*rdis/dd + 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 + 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 + 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 + endif cgrad do j=iii,jjj-1 cgrad do k=1,3 cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k) cgrad enddo cgrad enddo - do k=1,3 - ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) - ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) - enddo + 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 @@ -4343,7 +4427,7 @@ 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 c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2, @@ -4691,9 +4775,11 @@ C & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle), & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble), & sinph1ph2(maxdouble,maxdouble) - logical lprn /.false./, lprn1 /.false./ + logical lprn /.false./, lprn1 /.true./ etheta=0.0D0 do i=ithet_start,ithet_end + if ((itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or. + &(itype(i).eq.ntyp1)) cycle dethetai=0.0d0 dephii=0.0d0 dephii1=0.0d0 @@ -4844,9 +4930,11 @@ C enddo enddo 10 continue - if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') - & i,theta(i)*rad2deg,phii*rad2deg, +c lprn1=.true. + if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)') + & 'ebe', i,theta(i)*rad2deg,phii*rad2deg, & phii1*rad2deg,ethetai +c lprn1=.false. 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 @@ -5650,7 +5738,7 @@ C Proline-Proline pair is a special case... & 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) + write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) enddo ! 6/20/98 - dihedral angle constraints edihcnstr=0.0d0 @@ -5765,6 +5853,7 @@ c do i=1,ndih_constr else difi=0.0 endif +c write (iout,*) "gloci", gloc(i-3,icg) cd write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii, cd & rad2deg*phi0(i), rad2deg*drange(i), cd & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) @@ -5801,7 +5890,6 @@ c lprn=.true. 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) @@ -5836,6 +5924,7 @@ C Regular cosine and sine terms enddo gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*gloci1 gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*gloci2 +c write (iout,*) "gloci", gloc(i-3,icg) enddo return end @@ -5868,26 +5957,60 @@ C Set lprn=.true. for debugging c lprn=.true. c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor esccor=0.0D0 - do i=iphi_start,iphi_end + do i=itau_start,itau_end esccor_ii=0.0D0 - itori=itype(i-2) - itori1=itype(i-1) + if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle + 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) + + +c do intertyp=1,3 !intertyp + do intertyp=2,2 !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 - do j=1,nterm_sccor - v1ij=v1sccor(j,itori,itori1) - v2ij=v2sccor(j,itori,itori1) - cosphi=dcos(j*phii) - sinphi=dsin(j*phii) + 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,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6) + & (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_sc(2,i,icg), +c & gloc_sc(3,i,icg) +c enddo return end c---------------------------------------------------------------------------- @@ -8091,7 +8214,7 @@ c---------------------------------------------------------------------------- include 'COMMON.GEO' logical swap double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2), - & auxvec1(2),auxvec2(1),auxmat1(2,2) + & auxvec1(2),auxvec2(2),auxmat1(2,2) logical lprn common /kutas/ lprn CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC