X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc%2Fenergy_p_new.F;h=d857079aab6250551bc82e40915577cd83d9e78a;hb=5ff7ad0bbfd2c60edf49b10b9f9e6f81ff42a1e2;hp=bf5c3e7f0f2cefcec641ebb14fe080740c43a995;hpb=ca784a0624157f2a77b80ee7bcff288444176044;p=unres.git diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F index bf5c3e7..d857079 100644 --- a/source/wham/src/energy_p_new.F +++ b/source/wham/src/energy_p_new.F @@ -107,7 +107,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees & +wvdwpp*evdw1 & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d @@ -116,7 +116,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2 & +welec*fact(1)*(ees+evdw1) & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc - & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 + & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d @@ -154,6 +154,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t energia(19)=esccor energia(20)=edihcnstr energia(21)=evdw_t +c if (dyn_ss) call dyn_set_nss c detecting NaNQ #ifdef ISNAN #ifdef AIX @@ -770,6 +771,7 @@ C include 'COMMON.ENEPS' include 'COMMON.IOUNITS' include 'COMMON.CALC' + include 'COMMON.SBRIDGE' logical lprn common /srutu/icall integer icant @@ -800,6 +802,21 @@ C Calculate SC interaction energy. C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) +C in case of diagnostics write (iout,*) "TU SZUKAJ",i,j,dyn_ss_mask(i),dyn_ss_mask(j) +C /06/28/2013 Adasko: In case of dyn_ss - dynamic disulfide bond +C formation no electrostatic interactions should be calculated. If it +C would be allowed NaN would appear + IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN +C /06/28/2013 Adasko: dyn_ss_mask is logical statement wheather this Cys +C residue can or cannot form disulfide bond. There is still bug allowing +C Cys...Cys...Cys bond formation + call dyn_ssbond_ene(i,j,evdwij) +C /06/28/2013 Adasko: dyn_ssbond_ene is dynamic SS bond foration energy +C function in ssMD.F + evdw=evdw+evdwij +c if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') +c & 'evdw',i,j,evdwij,' ss' + ELSE ind=ind+1 itypj=itype(j) dscj_inv=vbld_inv(j+nres) @@ -866,6 +883,7 @@ c--------------------------------------------------------------- c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj, c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)), c & aux*e2/eps(itypi,itypj) +c write (iout,'(a6,2i5,0pf7.3)') 'evdw',i,j,evdwij if (lprn) then sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) epsi=bb(itypi,itypj)**2/aa(itypi,itypj) @@ -889,6 +907,7 @@ C Calculate the radial part of the gradient C Calculate angular part of the gradient. call sc_grad endif + ENDIF ! dyn_ss enddo ! j enddo ! iint enddo ! i @@ -2897,9 +2916,12 @@ 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 (.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 @@ -3032,11 +3054,12 @@ C 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 +c & +akct*deltad*deltat12 & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi -c write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, -c & " akct",akct," deltad",deltad," deltat",deltat1,deltat2, -c & " deltat12",deltat12," eij",eij + write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth, + & " akct",akct," deltad",deltad," deltat",deltat1,deltat2, + & " deltat12",deltat12," eij",eij,"ebr",ebr ed=2*akcm*deltad+akct*deltat12 pom1=akct*deltad pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi @@ -3081,6 +3104,7 @@ c include 'COMMON.FFIELD' include 'COMMON.CONTROL' double precision u(3),ud(3) + lprn=.false. estr=0.0d0 do i=nnt+1,nct diff = vbld(i)-vbldp0 @@ -3100,8 +3124,9 @@ c nbi=nbondterm(iti) if (nbi.eq.1) then diff=vbld(i+nres)-vbldsc0(1,iti) -c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, -c & AKSC(1,iti),AKSC(1,iti)*diff*diff + if (lprn) + & write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff, + & AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff do j=1,3 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) @@ -3130,8 +3155,9 @@ c & AKSC(1,iti),AKSC(1,iti)*diff*diff usum=usum+uprod1 usumsqder=usumsqder+ud(j)*uprod2 enddo -c write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), -c & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) + if (lprn) + & write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti), + & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi) estr=estr+uprod/usum do j=1,3 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres) @@ -4003,7 +4029,8 @@ c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) escloc = escloc + sumene c write (2,*) "escloc",escloc if (.not. calc_grad) goto 1 -#ifdef DEBUG + +#ifdef DEBUG2 C C This section to check the numerical derivatives of the energy of ith side C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert @@ -4463,24 +4490,16 @@ c lprn=.true. itori=itortyp(itype(i-2)) itori1=itortyp(itype(i-1)) itori2=itortyp(itype(i)) -c iblock=1 -c if (iabs(itype(i+1)).eq.20) iblock=2 phii=phi(i) phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 C Regular cosine and sine terms -c c do j=1,ntermd_1(itori,itori1,itori2,iblock) -c v1cij=v1c(1,j,itori,itori1,itori2,iblock) -c v1sij=v1s(1,j,itori,itori1,itori2,iblock) -c v2cij=v1c(2,j,itori,itori1,itori2,iblock) -c v2sij=v1s(2,j,itori,itori1,itori2,iblock) - do j=1,ntermd_1(itori,itori1,itori2) + do j=1,ntermd_1(itori,itori1,itori2) v1cij=v1c(1,j,itori,itori1,itori2) v1sij=v1s(1,j,itori,itori1,itori2) v2cij=v1c(2,j,itori,itori1,itori2) v2sij=v1s(2,j,itori,itori1,itori2) - cosphi1=dcos(j*phii) sinphi1=dsin(j*phii) cosphi2=dcos(j*phii1) @@ -4491,12 +4510,7 @@ c v2sij=v1s(2,j,itori,itori1,itori2,iblock) gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2) enddo do k=2,ntermd_2(itori,itori1,itori2) -c do k=2,ntermd_2(itori,itori1,itori2,iblock) do l=1,k-1 -c v1cdij = v2c(k,l,itori,itori1,itori2,iblock) -c v2cdij = v2c(l,k,itori,itori1,itori2,iblock) -c v1sdij = v2s(k,l,itori,itori1,itori2,iblock) -c v2sdij = v2s(l,k,itori,itori1,itori2,iblock) v1cdij = v2c(k,l,itori,itori1,itori2) v2cdij = v2c(l,k,itori,itori1,itori2) v1sdij = v2s(k,l,itori,itori1,itori2) @@ -6469,7 +6483,7 @@ 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