X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=source%2Fcluster%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=340af750858847e90a5298ccb7402b52ee59ec37;hb=455b2d37bc67ae119290e3e2048e0ab1df408fd2;hp=968a9f1b27fee332a97d7b127f12dab0f149f646;hpb=eee3a1e3f0ccd607d4ca71f73afaea1fb952a05c;p=unres.git diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F index 968a9f1..340af75 100644 --- a/source/cluster/wham/src-M/energy_p_new.F +++ b/source/cluster/wham/src-M/energy_p_new.F @@ -121,7 +121,15 @@ c print *,ecorr,ecorr5,ecorr6,eturn6 if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) endif - + if (nsaxs.gt.0 .and. saxs_mode.eq.0) then + call e_saxs(Esaxs_constr) +c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr + else if (nsaxs.gt.0 .and. saxs_mode.gt.0) then + call e_saxsC(Esaxs_constr) +c write (iout,*) "From EsaxsC: Esaxs_constr",Esaxs_constr + else + Esaxs_constr = 0.0d0 + endif c write(iout,*) "TEST_ENE",constr_homology if (constr_homology.ge.1) then call e_modeller(ehomology_constr) @@ -143,7 +151,7 @@ c write (iout,*) "ft(6)",fact(6),wliptran,eliptran & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr - & +wliptran*eliptran + & +wliptran*eliptran+wsaxs*esaxs_constr else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees & +wvdwpp*evdw1 @@ -153,7 +161,7 @@ c write (iout,*) "ft(6)",fact(6),wliptran,eliptran & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr - & +wliptran*eliptran + & +wliptran*eliptran+wsaxs*esaxs_constr endif #else if (shield_mode.gt.0) then @@ -165,7 +173,7 @@ c write (iout,*) "ft(6)",fact(6),wliptran,eliptran & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d & +wbond*estr+wsccor*fact(1)*esccor+ehomology_constr - & +wliptran*eliptran + & +wliptran*eliptran+wsaxs*esaxs_constr else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2 & +welec*fact(1)*(ees+evdw1) @@ -175,7 +183,7 @@ c write (iout,*) "ft(6)",fact(6),wliptran,eliptran & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr - & +wliptran*eliptran + & +wliptran*eliptran+wsaxs*esaxs_constr endif #endif @@ -212,6 +220,7 @@ c write (iout,*) "ft(6)",fact(6),wliptran,eliptran energia(20)=edihcnstr energia(24)=ehomology_constr energia(21)=evdw_t + energia(25)=Esaxs_constr c energia(24)=ethetacnstr energia(22)=eliptran c detecting NaNQ @@ -398,6 +407,7 @@ C------------------------------------------------------------------------ edihcnstr=energia(20) estr=energia(18) ehomology_constr=energia(24) + esaxs_constr=energia(25) c ethetacnstr=energia(24) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1, @@ -407,8 +417,8 @@ c ethetacnstr=energia(24) & ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5), & eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2), & eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5), - & esccor,wsccor*fact(1),edihcnstr,ehomology_constr,ebr*nss, - & etot + & esccor,wsccor*fact(1),edihcnstr,ehomology_constr, + & wsaxs*esaxs_constr,ebr*nss,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -431,6 +441,7 @@ c ethetacnstr=energia(24) & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/ + & 'E_SAXS=',1pE16.6,' (SAXS restraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'ETOT= ',1pE16.6,' (total)') #else @@ -440,7 +451,7 @@ c ethetacnstr=energia(24) & ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2), & eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3), & eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor, - & edihcnstr,ehomology_constr,ebr*nss, + & edihcnstr,ehomology_constr,esaxs_constr*wsaxs,ebr*nss, & etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ @@ -463,6 +474,7 @@ c ethetacnstr=energia(24) & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/ + & 'E_SAXS=',1pE16.6,' (SAXS restraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif @@ -1182,6 +1194,7 @@ C logical lprn integer icant external icant + integer xshift,yshift,zshift evdw=0.0D0 evdw_t=0.0d0 c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon @@ -2127,6 +2140,7 @@ C include 'COMMON.FFIELD' include 'COMMON.SHIELD' + integer xshift,yshift,zshift dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), @@ -3542,6 +3556,7 @@ C include 'COMMON.INTERACT' include 'COMMON.FFIELD' include 'COMMON.IOUNITS' + integer xshift,yshift,zshift dimension ggg(3) evdw2=0.0D0 evdw2_14=0.0d0 @@ -9333,7 +9348,7 @@ C gradient po costhet & )*wshield C grad_shield_side is Cbeta sidechain gradient grad_shield_side(j,ishield_list(i),i)= - & (sh_frac_dist_grad(j)*-2.0d0 + & (sh_frac_dist_grad(j)*(-2.0d0) & *VofOverlap & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( @@ -9501,7 +9516,7 @@ C gradient po costhet &*VofOverlap C grad_shield_side is Cbeta sidechain gradient grad_shield_side(j,ishield_list(i),i)= - & (sh_frac_dist_grad(j)*-2.0d0 + & (sh_frac_dist_grad(j)*(-2.0d0) & +scale_fac_dist*costhet_grad(j)*2.0d0/(1.0-costhet) & +scale_fac_dist*(cosphi_grad_long(j)) & *2.0d0/(1.0-cosphi)) @@ -9666,4 +9681,351 @@ C eliptran=elpitran+0.0 ! I am in water enddo return end -C------------------------------------------------------------------------------------- +c---------------------------------------------------------------------------- + subroutine e_saxs(Esaxs_constr) + implicit none + include 'DIMENSIONS' +#ifdef MPI + include "mpif.h" + include "COMMON.SETUP" + integer IERR +#endif + include 'COMMON.SBRIDGE' + include 'COMMON.CHAIN' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.INTERACT' + include 'COMMON.VAR' + include 'COMMON.IOUNITS' + include 'COMMON.DERIV' + include 'COMMON.CONTROL' + include 'COMMON.NAMES' + include 'COMMON.FFIELD' + include 'COMMON.LANGEVIN' +c + double precision Esaxs_constr + integer i,iint,j,k,l + double precision PgradC(maxSAXS,3,maxres), + & PgradX(maxSAXS,3,maxres),Pcalc(maxSAXS) +#ifdef MPI + double precision PgradC_(maxSAXS,3,maxres), + & PgradX_(maxSAXS,3,maxres),Pcalc_(maxSAXS) +#endif + double precision dk,dijCACA,dijCASC,dijSCCA,dijSCSC, + & sigma2CACA,sigma2CASC,sigma2SCCA,sigma2SCSC,expCACA,expCASC, + & expSCCA,expSCSC,CASCgrad,SCCAgrad,SCSCgrad,aux,auxC,auxC1, + & auxX,auxX1,CACAgrad,Cnorm + double precision dist + external dist +c SAXS restraint penalty function +#ifdef DEBUG + write(iout,*) "------- SAXS penalty function start -------" + write (iout,*) "nsaxs",nsaxs + write (iout,*) "Esaxs: iatsc_s",iatsc_s," iatsc_e",iatsc_e + write (iout,*) "Psaxs" + do i=1,nsaxs + write (iout,'(i5,e15.5)') i, Psaxs(i) + enddo +#endif + Esaxs_constr = 0.0d0 + do k=1,nsaxs + Pcalc(k)=0.0d0 + do j=1,nres + do l=1,3 + PgradC(k,l,j)=0.0d0 + PgradX(k,l,j)=0.0d0 + enddo + enddo + enddo + do i=iatsc_s,iatsc_e + do iint=1,nint_gr(i) + do j=istart(i,iint),iend(i,iint) +#ifdef ALLSAXS + dijCACA=dist(i,j) + dijCASC=dist(i,j+nres) + dijSCCA=dist(i+nres,j) + dijSCSC=dist(i+nres,j+nres) + sigma2CACA=2.0d0/(pstok**2) + sigma2CASC=4.0d0/(pstok**2+restok(itype(j))**2) + sigma2SCCA=4.0d0/(pstok**2+restok(itype(i))**2) + sigma2SCSC=4.0d0/(restok(itype(j))**2+restok(itype(i))**2) + do k=1,nsaxs + dk = distsaxs(k) + expCACA = dexp(-0.5d0*sigma2CACA*(dijCACA-dk)**2) + if (itype(j).ne.10) then + expCASC = dexp(-0.5d0*sigma2CASC*(dijCASC-dk)**2) + else + endif + expCASC = 0.0d0 + if (itype(i).ne.10) then + expSCCA = dexp(-0.5d0*sigma2SCCA*(dijSCCA-dk)**2) + else + expSCCA = 0.0d0 + endif + if (itype(i).ne.10 .and. itype(j).ne.10) then + expSCSC = dexp(-0.5d0*sigma2SCSC*(dijSCSC-dk)**2) + else + expSCSC = 0.0d0 + endif + Pcalc(k) = Pcalc(k)+expCACA+expCASC+expSCCA+expSCSC +#ifdef DEBUG + write(iout,*) "i j k Pcalc",i,j,Pcalc(k) +#endif + CACAgrad = sigma2CACA*(dijCACA-dk)*expCACA + CASCgrad = sigma2CASC*(dijCASC-dk)*expCASC + SCCAgrad = sigma2SCCA*(dijSCCA-dk)*expSCCA + SCSCgrad = sigma2SCSC*(dijSCSC-dk)*expSCSC + do l=1,3 +c CA CA + aux = CACAgrad*(C(l,j)-C(l,i))/dijCACA + PgradC(k,l,i) = PgradC(k,l,i)-aux + PgradC(k,l,j) = PgradC(k,l,j)+aux +c CA SC + if (itype(j).ne.10) then + aux = CASCgrad*(C(l,j+nres)-C(l,i))/dijCASC + PgradC(k,l,i) = PgradC(k,l,i)-aux + PgradC(k,l,j) = PgradC(k,l,j)+aux + PgradX(k,l,j) = PgradX(k,l,j)+aux + endif +c SC CA + if (itype(i).ne.10) then + aux = SCCAgrad*(C(l,j)-C(l,i+nres))/dijSCCA + PgradX(k,l,i) = PgradX(k,l,i)-aux + PgradC(k,l,i) = PgradC(k,l,i)-aux + PgradC(k,l,j) = PgradC(k,l,j)+aux + endif +c SC SC + if (itype(i).ne.10 .and. itype(j).ne.10) then + aux = SCSCgrad*(C(l,j+nres)-C(l,i+nres))/dijSCSC + PgradC(k,l,i) = PgradC(k,l,i)-aux + PgradC(k,l,j) = PgradC(k,l,j)+aux + PgradX(k,l,i) = PgradX(k,l,i)-aux + PgradX(k,l,j) = PgradX(k,l,j)+aux + endif + enddo ! l + enddo ! k +#else + dijCACA=dist(i,j) + sigma2CACA=0.25d0/(restok(itype(j))**2+restok(itype(i))**2) + do k=1,nsaxs + dk = distsaxs(k) + expCACA = dexp(-0.5d0*sigma2CACA*(dijCACA-dk)**2) + Pcalc(k) = Pcalc(k)+expCACA +#ifdef DEBUG + write(iout,*) "i j k Pcalc",i,j,Pcalc(k) +#endif + CACAgrad = sigma2CACA*(dijCACA-dk)*expCACA + do l=1,3 +c CA CA + aux = CACAgrad*(C(l,j)-C(l,i))/dijCACA + PgradC(k,l,i) = PgradC(k,l,i)-aux + PgradC(k,l,j) = PgradC(k,l,j)+aux + enddo ! l + enddo ! k +#endif + enddo ! j + enddo ! iint + enddo ! i +#ifdef MPI + if (nfgtasks.gt.1) then + call MPI_Reduce(Pcalc(1),Pcalc_(1),nsaxs,MPI_DOUBLE_PRECISION, + & MPI_SUM,king,FG_COMM,IERR) + if (fg_rank.eq.king) then + do k=1,nsaxs + Pcalc(k) = Pcalc_(k) + enddo + endif + call MPI_Reduce(PgradC(k,1,1),PgradC_(k,1,1),3*maxsaxs*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + if (fg_rank.eq.king) then + do i=1,nres + do l=1,3 + do k=1,nsaxs + PgradC(k,l,i) = PgradC_(k,l,i) + enddo + enddo + enddo + endif +#ifdef ALLSAXS + call MPI_Reduce(PgradX(k,1,1),PgradX_(k,1,1),3*maxsaxs*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + if (fg_rank.eq.king) then + do i=1,nres + do l=1,3 + do k=1,nsaxs + PgradX(k,l,i) = PgradX_(k,l,i) + enddo + enddo + enddo + endif +#endif + endif +#endif +#ifdef MPI + if (fg_rank.eq.king) then +#endif + Cnorm = 0.0d0 + do k=1,nsaxs + Cnorm = Cnorm + Pcalc(k) + enddo + Esaxs_constr = dlog(Cnorm) + do k=1,nsaxs + Esaxs_constr = Esaxs_constr - Psaxs(k)*dlog(Pcalc(k)) +#ifdef DEBUG + write (iout,*) "k",k," Esaxs_constr",Esaxs_constr +#endif + enddo +#ifdef DEBUG + write (iout,*) "Cnorm",Cnorm," Esaxs_constr",Esaxs_constr +#endif + do i=nnt,nct + do l=1,3 + auxC=0.0d0 + auxC1=0.0d0 + auxX=0.0d0 + auxX1=0.d0 + do k=1,nsaxs + auxC = auxC +Psaxs(k)*PgradC(k,l,i)/Pcalc(k) + auxC1 = auxC1+PgradC(k,l,i) +#ifdef ALLSAXS + auxX = auxX +Psaxs(k)*PgradX(k,l,i)/Pcalc(k) + auxX1 = auxX1+PgradX(k,l,i) +#endif + enddo + gsaxsC(l,i) = auxC - auxC1/Cnorm +#ifdef ALLSAXS + gsaxsX(l,i) = auxX - auxX1/Cnorm +#endif +c write (iout,*) "l i",l,i," gradC",wsaxs*(auxC - auxC1/Cnorm), +c * " gradX",wsaxs*(auxX - auxX1/Cnorm) + enddo + enddo +#ifdef MPI + endif +#endif + return + end +c---------------------------------------------------------------------------- + subroutine e_saxsC(Esaxs_constr) + implicit none + include 'DIMENSIONS' +#ifdef MPI + include "mpif.h" + include "COMMON.SETUP" + integer IERR +#endif + include 'COMMON.SBRIDGE' + include 'COMMON.CHAIN' + include 'COMMON.INTERACT' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.VAR' + include 'COMMON.IOUNITS' + include 'COMMON.DERIV' + include 'COMMON.CONTROL' + include 'COMMON.NAMES' + include 'COMMON.FFIELD' + include 'COMMON.LANGEVIN' +c + double precision Esaxs_constr + integer i,iint,j,k,l + double precision PgradC(3,maxres),PgradX(3,maxres),Pcalc,logPtot +#ifdef MPI + double precision gsaxsc_(3,maxres),gsaxsx_(3,maxres),logPtot_ +#endif + double precision dk,dijCASPH,dijSCSPH, + & sigma2CA,sigma2SC,expCASPH,expSCSPH, + & CASPHgrad,SCSPHgrad,aux,auxC,auxC1, + & auxX,auxX1,Cnorm +c SAXS restraint penalty function +#ifdef DEBUG + write(iout,*) "------- SAXS penalty function start -------" + write (iout,*) "nsaxs",nsaxs," isaxs_start",isaxs_start, + & " isaxs_end",isaxs_end + write (iout,*) "nnt",nnt," ntc",nct + do i=nnt,nct + write(iout,'(a6,i5,3f10.5,5x,2f10.5)') + & "CA",i,(C(j,i),j=1,3),pstok,restok(itype(i)) + enddo + do i=nnt,nct + write(iout,'(a6,i5,3f10.5)')"CSaxs",i,(Csaxs(j,i),j=1,3) + enddo +#endif + Esaxs_constr = 0.0d0 + logPtot=0.0d0 + do j=isaxs_start,isaxs_end + Pcalc=0.0d0 + do i=1,nres + do l=1,3 + PgradC(l,i)=0.0d0 + PgradX(l,i)=0.0d0 + enddo + enddo + do i=nnt,nct + dijCASPH=0.0d0 + dijSCSPH=0.0d0 + do l=1,3 + dijCASPH=dijCASPH+(C(l,i)-Csaxs(l,j))**2 + enddo + if (itype(i).ne.10) then + do l=1,3 + dijSCSPH=dijSCSPH+(C(l,i+nres)-Csaxs(l,j))**2 + enddo + endif + sigma2CA=2.0d0/pstok**2 + sigma2SC=4.0d0/restok(itype(i))**2 + expCASPH = dexp(-0.5d0*sigma2CA*dijCASPH) + expSCSPH = dexp(-0.5d0*sigma2SC*dijSCSPH) + Pcalc = Pcalc+expCASPH+expSCSPH +#ifdef DEBUG + write(*,*) "processor i j Pcalc", + & MyRank,i,j,dijCASPH,dijSCSPH, Pcalc +#endif + CASPHgrad = sigma2CA*expCASPH + SCSPHgrad = sigma2SC*expSCSPH + do l=1,3 + aux = (C(l,i+nres)-Csaxs(l,j))*SCSPHgrad + PgradX(l,i) = PgradX(l,i) + aux + PgradC(l,i) = PgradC(l,i)+(C(l,i)-Csaxs(l,j))*CASPHgrad+aux + enddo ! l + enddo ! i + do i=nnt,nct + do l=1,3 + gsaxsc(l,i)=gsaxsc(l,i)+PgradC(l,i)/Pcalc + gsaxsx(l,i)=gsaxsx(l,i)+PgradX(l,i)/Pcalc + enddo + enddo + logPtot = logPtot - dlog(Pcalc) +c print *,"me",me,MyRank," j",j," logPcalc",-dlog(Pcalc), +c & " logPtot",logPtot + enddo ! j +#ifdef MPI + if (nfgtasks.gt.1) then +c write (iout,*) "logPtot before reduction",logPtot + call MPI_Reduce(logPtot,logPtot_,1,MPI_DOUBLE_PRECISION, + & MPI_SUM,king,FG_COMM,IERR) + logPtot = logPtot_ +c write (iout,*) "logPtot after reduction",logPtot + call MPI_Reduce(gsaxsC(1,1),gsaxsC_(1,1),3*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + if (fg_rank.eq.king) then + do i=1,nres + do l=1,3 + gsaxsC(l,i) = gsaxsC_(l,i) + enddo + enddo + endif + call MPI_Reduce(gsaxsX(1,1),gsaxsX_(1,1),3*nres, + & MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) + if (fg_rank.eq.king) then + do i=1,nres + do l=1,3 + gsaxsX(l,i) = gsaxsX_(l,i) + enddo + enddo + endif + endif +#endif + Esaxs_constr = logPtot + return + end