X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc-HCD-5D%2Fenergy_p_new_barrier.F;h=ddc2a4d30adba53249de9fdcba24166dd3d36ba7;hb=de4daf245936d67b5c08eb584fca985adab9928e;hp=ba7cbd8bf6ae65e67eecaf05d3e8074cd24885ac;hpb=cf4da5a9f21b849afd840360ba40787a35583c71;p=unres.git diff --git a/source/unres/src-HCD-5D/energy_p_new_barrier.F b/source/unres/src-HCD-5D/energy_p_new_barrier.F index ba7cbd8..ddc2a4d 100644 --- a/source/unres/src-HCD-5D/energy_p_new_barrier.F +++ b/source/unres/src-HCD-5D/energy_p_new_barrier.F @@ -115,6 +115,7 @@ c call chainbuild_cart if (nfgtasks.gt.1) then call MPI_Bcast(itime_mat,1,MPI_INT,king,FG_COMM,IERROR) endif +c write (iout,*) "itime_mat",itime_mat," imatupdate",imatupdate if (mod(itime_mat,imatupdate).eq.0) then call make_SCp_inter_list call make_SCSC_inter_list @@ -1476,6 +1477,7 @@ C & sigij,r0ij,rcut,sqrij,sss1,sssgrad1 double precision fcont,fprimcont double precision sscale,sscagrad + double precision boxshift c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 c do i=iatsc_s,iatsc_e @@ -1488,6 +1490,7 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) + call to_box(xi,yi,zi) C Change 12/1/95 num_conti=0 C @@ -1499,9 +1502,13 @@ cd & 'iend=',iend(i,iint) c do j=istart(i,iint),iend(i,iint) itypj=iabs(itype(j)) if (itypj.eq.ntyp1) cycle - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) C Change 12/1/95 to calculate four-body interactions rij=xj*xj+yj*yj+zj*zj rrij=1.0D0/rij @@ -1649,6 +1656,7 @@ C & fac_augm,e_augm,r_inv_ij,r_shift_inv,sss1,sssgrad1 logical scheck double precision sscale,sscagrad + double precision boxshift c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 c do i=iatsc_s,iatsc_e @@ -1661,6 +1669,7 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) + call to_box(xi,yi,zi) C C Calculate SC interaction energy. C @@ -1668,9 +1677,13 @@ c do iint=1,nint_gr(i) c do j=istart(i,iint),iend(i,iint) itypj=iabs(itype(j)) if (itypj.eq.ntyp1) cycle - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) rrij=1.0D0/(xj*xj+yj*yj+zj*zj) fac_augm=rrij**expon e_augm=augm(itypi,itypj)*fac_augm @@ -1748,6 +1761,7 @@ C double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,xi,yi,zi, & sss1,sssgrad1 double precision sscale,sscagrad + double precision boxshift c double precision rrsave(maxdim) logical lprn evdw=0.0D0 @@ -1769,6 +1783,7 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) + call to_box(xi,yi,zi) dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -1803,9 +1818,13 @@ c chip12=0.0D0 c alf1=0.0D0 c alf2=0.0D0 c alf12=0.0D0 - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) dxj=dc_norm(1,nres+j) dyj=dc_norm(2,nres+j) dzj=dc_norm(3,nres+j) @@ -1882,14 +1901,13 @@ C include 'COMMON.SPLITELE' include 'COMMON.SBRIDGE' logical lprn - integer xshift,yshift,zshift,subchap double precision evdw integer itypi,itypj,itypi1,iint,ind,ikont 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 + & sslipj,ssgradlipj,ssgradlipi,sig,rij_shift,faclip double precision dist,sscale,sscagrad,sscagradlip,sscalelip + double precision boxshift evdw=0.0D0 ccccc energy_dec=.false. C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon @@ -1912,66 +1930,14 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) -C Return atom into box, boxxsize is size of box in x dimension -c 134 continue -c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize -c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize -C Condition for being inside the proper box -c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or. -c & (xi.lt.((xshift-0.5d0)*boxxsize))) then -c go to 134 -c endif -c 135 continue -c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize -c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize -C Condition for being inside the proper box -c if ((yi.gt.((yshift+0.5d0)*boxysize)).or. -c & (yi.lt.((yshift-0.5d0)*boxysize))) then -c go to 135 -c endif -c 136 continue -c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize -c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize -C Condition for being inside the proper box -c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or. -c & (zi.lt.((zshift-0.5d0)*boxzsize))) then -c go to 136 -c endif - xi=mod(xi,boxxsize) - if (xi.lt.0) xi=xi+boxxsize - yi=mod(yi,boxysize) - if (yi.lt.0) yi=yi+boxysize - zi=mod(zi,boxzsize) - if (zi.lt.0) zi=zi+boxzsize + call to_box(xi,yi,zi) C define scaling factor for lipids C if (positi.le.0) positi=positi+boxzsize C print *,i C first for peptide groups c for each residue check if it is in lipid or lipid water border area - if ((zi.gt.bordlipbot) - &.and.(zi.lt.bordliptop)) then -C the energy transfer exist - if (zi.lt.buflipbot) then -C what fraction I am in - fracinbuf=1.0d0- - & ((zi-bordlipbot)/lipbufthick) -C lipbufthick is thickenes of lipid buffore - sslipi=sscalelip(fracinbuf) - ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick - elseif (zi.gt.bufliptop) then - fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) - sslipi=sscalelip(fracinbuf) - ssgradlipi=sscagradlip(fracinbuf)/lipbufthick - else - sslipi=1.0d0 - ssgradlipi=0.0 - endif - else - sslipi=0.0d0 - ssgradlipi=0.0 - endif - + call lipid_layer(xi,yi,zi,sslipi,ssgradlipi) C xi=xi+xshift*boxxsize C yi=yi+yshift*boxysize C zi=zi+zshift*boxzsize @@ -1998,15 +1964,15 @@ c write(iout,*) "PO ZWYKLE", evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' C triple bond artifac removal - do k=j+1,iend(i,iint) + do k=j+1,iend(i,iint) C search over all next residues - if (dyn_ss_mask(k)) then + if (dyn_ss_mask(k)) then C check if they are cysteins C write(iout,*) 'k=',k c write(iout,*) "PRZED TRI", evdwij - evdwij_przed_tri=evdwij - call triple_ssbond_ene(i,j,k,evdwij) + evdwij_przed_tri=evdwij + call triple_ssbond_ene(i,j,k,evdwij) c if(evdwij_przed_tri.ne.evdwij) then c write (iout,*) "TRI:", evdwij, evdwij_przed_tri c endif @@ -2014,30 +1980,30 @@ c endif c write(iout,*) "PO TRI", evdwij C call the energy function that removes the artifical triple disulfide C bond the soubroutine is located in ssMD.F - evdw=evdw+evdwij - if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,'tss' - endif!dyn_ss_mask(k) - enddo! k + endif!dyn_ss_mask(k) + enddo! k ELSE - ind=ind+1 - itypj=iabs(itype(j)) - if (itypj.eq.ntyp1) cycle + ind=ind+1 + itypj=iabs(itype(j)) + if (itypj.eq.ntyp1) cycle c dscj_inv=dsc_inv(itypj) - dscj_inv=vbld_inv(j+nres) + dscj_inv=vbld_inv(j+nres) c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv, c & 1.0d0/vbld(j+nres) c write (iout,*) "i",i," j", j," itype",itype(i),itype(j) - sig0ij=sigma(itypi,itypj) - chi1=chi(itypi,itypj) - chi2=chi(itypj,itypi) - chi12=chi1*chi2 - chip1=chip(itypi) - chip2=chip(itypj) - chip12=chip1*chip2 - alf1=alp(itypi) - alf2=alp(itypj) - alf12=0.5D0*(alf1+alf2) + sig0ij=sigma(itypi,itypj) + chi1=chi(itypi,itypj) + chi2=chi(itypj,itypi) + chi12=chi1*chi2 + chip1=chip(itypi) + chip2=chip(itypj) + chip12=chip1*chip2 + alf1=alp(itypi) + alf2=alp(itypj) + alf12=0.5D0*(alf1+alf2) C For diagnostics only!!! c chi1=0.0D0 c chi2=0.0D0 @@ -2048,191 +2014,112 @@ c chip12=0.0D0 c alf1=0.0D0 c alf2=0.0D0 c alf12=0.0D0 - xj=c(1,nres+j) - yj=c(2,nres+j) - zj=c(3,nres+j) -C Return atom J into box the original box -c 137 continue -c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize -c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize -C Condition for being inside the proper box -c if ((xj.gt.((0.5d0)*boxxsize)).or. -c & (xj.lt.((-0.5d0)*boxxsize))) then -c go to 137 -c endif -c 138 continue -c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize -c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize -C Condition for being inside the proper box -c if ((yj.gt.((0.5d0)*boxysize)).or. -c & (yj.lt.((-0.5d0)*boxysize))) then -c go to 138 -c endif -c 139 continue -c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize -c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize -C Condition for being inside the proper box -c if ((zj.gt.((0.5d0)*boxzsize)).or. -c & (zj.lt.((-0.5d0)*boxzsize))) then -c go to 139 -c endif - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize - if ((zj.gt.bordlipbot) - &.and.(zj.lt.bordliptop)) then -C the energy transfer exist - if (zj.lt.buflipbot) then -C what fraction I am in - fracinbuf=1.0d0- - & ((zj-bordlipbot)/lipbufthick) -C lipbufthick is thickenes of lipid buffore - sslipj=sscalelip(fracinbuf) - ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick - elseif (zj.gt.bufliptop) then - fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) - sslipj=sscalelip(fracinbuf) - ssgradlipj=sscagradlip(fracinbuf)/lipbufthick - else - sslipj=1.0d0 - ssgradlipj=0.0 - endif - else - sslipj=0.0d0 - ssgradlipj=0.0 - endif - aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 - & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 - bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 - & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + call to_box(xj,yj,zj) + call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) + aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 C write(iout,*) "tu,", i,j,aa_lip(itypi,itypj),bb_lip(itypi,itypj) C if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)') C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) C if (ssgradlipj.gt.0.0d0) print *,"??WTF??" C print *,sslipi,sslipj,bordlipbot,zi,zj - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - subchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - subchap=1 - endif - enddo - enddo - enddo - if (subchap.eq.1) then - xj=xj_temp-xi - yj=yj_temp-yi - zj=zj_temp-zi - else - xj=xj_safe-xi - yj=yj_safe-yi - zj=zj_safe-zi - endif - dxj=dc_norm(1,nres+j) - dyj=dc_norm(2,nres+j) - dzj=dc_norm(3,nres+j) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + dxj=dc_norm(1,nres+j) + dyj=dc_norm(2,nres+j) + dzj=dc_norm(3,nres+j) C xj=xj-xi C yj=yj-yi C zj=zj-zi c write (iout,*) "dcnorj",dxi*dxi+dyi*dyi+dzi*dzi c write (iout,*) "j",j," dc_norm", 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,r_cut_int) + rrij=1.0D0/(xj*xj+yj*yj+zj*zj) + rij=dsqrt(rrij) + 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.eq.0.0d0) cycle - sssgrad=sscagrad(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 - sigsq=1.0D0/sigsq - sig=sig0ij*dsqrt(sigsq) - rij_shift=1.0D0/rij-sig+sig0ij + call sc_angular + sigsq=1.0D0/sigsq + sig=sig0ij*dsqrt(sigsq) + rij_shift=1.0D0/rij-sig+sig0ij c for diagnostics; uncomment c rij_shift=1.2*sig0ij C I hate to put IF's in the loops, but here don't have another choice!!!! - if (rij_shift.le.0.0D0) then - evdw=1.0D20 + if (rij_shift.le.0.0D0) then + evdw=1.0D20 cd write (iout,'(2(a3,i3,2x),17(0pf7.3))') cd & restyp(itypi),i,restyp(itypj),j, cd & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) - return - endif - sigder=-sig*sigsq + return + endif + sigder=-sig*sigsq c--------------------------------------------------------------- - rij_shift=1.0D0/rij_shift - fac=rij_shift**expon + rij_shift=1.0D0/rij_shift + fac=rij_shift**expon C here to start with C if (c(i,3).gt. - faclip=fac - e1=fac*fac*aa - e2=fac*bb - evdwij=eps1*eps2rt*eps3rt*(e1+e2) - eps2der=evdwij*eps3rt - eps3der=evdwij*eps2rt + faclip=fac + e1=fac*fac*aa + e2=fac*bb + evdwij=eps1*eps2rt*eps3rt*(e1+e2) + eps2der=evdwij*eps3rt + eps3der=evdwij*eps2rt C write(63,'(2i3,2e10.3,2f10.5)') i,j,aa,bb, evdwij, C &((sslipi+sslipj)/2.0d0+ C &(2.0d0-sslipi-sslipj)/2.0d0) c write (iout,*) "sigsq",sigsq," sig",sig," eps2rt",eps2rt, c & " eps3rt",eps3rt," eps1",eps1," e1",e1," e2",e2 - evdwij=evdwij*eps2rt*eps3rt - evdw=evdw+evdwij*sss - if (lprn) then - sigm=dabs(aa/bb)**(1.0D0/6.0D0) - epsi=bb**2/aa - write (iout,'(2(a3,i3,2x),17(0pf7.3))') - & restyp(itypi),i,restyp(itypj),j, - & epsi,sigm,chi1,chi2,chip1,chip2, - & eps1,eps2rt**2,eps3rt**2,sig,sig0ij, - & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, - & evdwij - endif + evdwij=evdwij*eps2rt*eps3rt + evdw=evdw+evdwij*sss + if (lprn) then + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa + write (iout,'(2(a3,i3,2x),17(0pf7.3))') + & restyp(itypi),i,restyp(itypj),j, + & epsi,sigm,chi1,chi2,chip1,chip2, + & eps1,eps2rt**2,eps3rt**2,sig,sig0ij, + & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, + & evdwij + endif - if (energy_dec) write (iout,'(a,2i5,3f10.5)') + if (energy_dec) write (iout,'(a,2i5,3f10.5)') & 'r sss evdw',i,j,1.0d0/rij,sss,evdwij C Calculate gradient components. - e1=e1*eps1*eps2rt**2*eps3rt**2 - fac=-expon*(e1+evdwij)*rij_shift - sigder=fac*sigder - fac=rij*fac + e1=e1*eps1*eps2rt**2*eps3rt**2 + fac=-expon*(e1+evdwij)*rij_shift + sigder=fac*sigder + fac=rij*fac c print '(2i4,6f8.4)',i,j,sss,sssgrad* c & evdwij,fac,sigma(itypi,itypj),expon - fac=fac+evdwij*sssgrad/sss*rij + fac=fac+evdwij*sssgrad/sss*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))) - gg_lipj(3)=ssgradlipj*gg_lipi(3) - gg_lipi(3)=gg_lipi(3)*ssgradlipi + 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))) + gg_lipj(3)=ssgradlipj*gg_lipi(3) + gg_lipi(3)=gg_lipi(3)*ssgradlipi C gg_lipi(3)=0.0d0 C gg_lipj(3)=0.0d0 - gg(1)=xj*fac - gg(2)=yj*fac - gg(3)=zj*fac + gg(1)=xj*fac + gg(2)=yj*fac + gg(3)=zj*fac C Calculate angular part of the gradient. c call sc_grad_scale(sss) - call sc_grad + call sc_grad ENDIF ! dyn_ss c enddo ! j c enddo ! iint @@ -2262,7 +2149,7 @@ C include 'COMMON.IOUNITS' include 'COMMON.CALC' include 'COMMON.SPLITELE' - integer xshift,yshift,zshift,subchap + double precision boxshift integer icall common /srutu/ icall logical lprn @@ -2271,8 +2158,7 @@ C 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 + & sslipj,ssgradlipj,ssgradlipi,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 @@ -2290,41 +2176,14 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) - xi=mod(xi,boxxsize) - if (xi.lt.0) xi=xi+boxxsize - yi=mod(yi,boxysize) - if (yi.lt.0) yi=yi+boxysize - zi=mod(zi,boxzsize) - if (zi.lt.0) zi=zi+boxzsize + call to_box(xi,yi,zi) C define scaling factor for lipids C if (positi.le.0) positi=positi+boxzsize C print *,i C first for peptide groups c for each residue check if it is in lipid or lipid water border area - if ((zi.gt.bordlipbot) - &.and.(zi.lt.bordliptop)) then -C the energy transfer exist - if (zi.lt.buflipbot) then -C what fraction I am in - fracinbuf=1.0d0- - & ((zi-bordlipbot)/lipbufthick) -C lipbufthick is thickenes of lipid buffore - sslipi=sscalelip(fracinbuf) - ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick - elseif (zi.gt.bufliptop) then - fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) - sslipi=sscalelip(fracinbuf) - ssgradlipi=sscagradlip(fracinbuf)/lipbufthick - else - sslipi=1.0d0 - ssgradlipi=0.0 - endif - else - sslipi=0.0d0 - ssgradlipi=0.0 - endif - + call lipid_layer(xi,yi,zi,sslipi,ssgradlipi) dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -2361,131 +2220,77 @@ c chip12=0.0D0 c alf1=0.0D0 c alf2=0.0D0 c alf12=0.0D0 -C xj=c(1,nres+j)-xi -C yj=c(2,nres+j)-yi -C zj=c(3,nres+j)-zi - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize - if ((zj.gt.bordlipbot) - &.and.(zj.lt.bordliptop)) then -C the energy transfer exist - if (zj.lt.buflipbot) then -C what fraction I am in - fracinbuf=1.0d0- - & ((zj-bordlipbot)/lipbufthick) -C lipbufthick is thickenes of lipid buffore - sslipj=sscalelip(fracinbuf) - ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick - elseif (zj.gt.bufliptop) then - fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) - sslipj=sscalelip(fracinbuf) - ssgradlipj=sscagradlip(fracinbuf)/lipbufthick - else - sslipj=1.0d0 - ssgradlipj=0.0 - endif - else - sslipj=0.0d0 - ssgradlipj=0.0 - endif - aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 - & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 - bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 - & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + call to_box(xj,yj,zj) + call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) + aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 + & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5') C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) C write(iout,*) "tu,", i,j,aa,bb,aa_lip(itypi,itypj),sslipi,sslipj - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - subchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - subchap=1 - endif - enddo - enddo - enddo - if (subchap.eq.1) then - xj=xj_temp-xi - yj=yj_temp-yi - zj=zj_temp-zi - else - xj=xj_safe-xi - yj=yj_safe-yi - zj=zj_safe-zi - endif - dxj=dc_norm(1,nres+j) - dyj=dc_norm(2,nres+j) - 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) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + dxj=dc_norm(1,nres+j) + dyj=dc_norm(2,nres+j) + 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 - sigsq=1.0D0/sigsq - sig=sig0ij*dsqrt(sigsq) - rij_shift=1.0D0/rij-sig+r0ij + call sc_angular + sigsq=1.0D0/sigsq + sig=sig0ij*dsqrt(sigsq) + rij_shift=1.0D0/rij-sig+r0ij C I hate to put IF's in the loops, but here don't have another choice!!!! - if (rij_shift.le.0.0D0) then - evdw=1.0D20 - return - endif - sigder=-sig*sigsq + if (rij_shift.le.0.0D0) then + evdw=1.0D20 + return + endif + sigder=-sig*sigsq c--------------------------------------------------------------- - rij_shift=1.0D0/rij_shift - fac=rij_shift**expon - e1=fac*fac*aa - e2=fac*bb - evdwij=eps1*eps2rt*eps3rt*(e1+e2) - eps2der=evdwij*eps3rt - eps3der=evdwij*eps2rt - fac_augm=rrij**expon - e_augm=augm(itypi,itypj)*fac_augm - evdwij=evdwij*eps2rt*eps3rt - evdw=evdw+evdwij+e_augm - if (lprn) then - sigm=dabs(aa/bb)**(1.0D0/6.0D0) - epsi=bb**2/aa - write (iout,'(2(a3,i3,2x),17(0pf7.3))') + rij_shift=1.0D0/rij_shift + fac=rij_shift**expon + e1=fac*fac*aa + e2=fac*bb + evdwij=eps1*eps2rt*eps3rt*(e1+e2) + eps2der=evdwij*eps3rt + eps3der=evdwij*eps2rt + fac_augm=rrij**expon + e_augm=augm(itypi,itypj)*fac_augm + evdwij=evdwij*eps2rt*eps3rt + evdw=evdw+evdwij+e_augm + if (lprn) then + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa + write (iout,'(2(a3,i3,2x),17(0pf7.3))') & restyp(itypi),i,restyp(itypj),j, & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0), & chi1,chi2,chip1,chip2, & eps1,eps2rt**2,eps3rt**2, & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, & evdwij+e_augm - endif + endif C Calculate gradient components. - e1=e1*eps1*eps2rt**2*eps3rt**2 - fac=-expon*(e1+evdwij)*rij_shift - sigder=fac*sigder - fac=rij*fac-2*expon*rrij*e_augm - fac=fac+(evdwij+e_augm)*sssgrad/sss*rij + e1=e1*eps1*eps2rt**2*eps3rt**2 + fac=-expon*(e1+evdwij)*rij_shift + sigder=fac*sigder + fac=rij*fac-2*expon*rrij*e_augm + fac=fac+(evdwij+e_augm)*sssgrad/sss*rij C Calculate the radial part of the gradient - gg(1)=xj*fac - gg(2)=yj*fac - gg(3)=zj*fac + gg(1)=xj*fac + gg(2)=yj*fac + gg(3)=zj*fac C Calculate angular part of the gradient. c call sc_grad_scale(sss) - call sc_grad + call sc_grad c enddo ! j c enddo ! iint enddo ! i @@ -2636,6 +2441,7 @@ C include 'COMMON.IOUNITS' c include 'COMMON.CONTACTS' dimension gg(3) + double precision boxshift cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct evdw=0.0D0 c do i=iatsc_s,iatsc_e @@ -2648,6 +2454,7 @@ c do i=iatsc_s,iatsc_e xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) + call to_box(xi,yi,zi) C C Calculate SC interaction energy. C @@ -2657,9 +2464,9 @@ cd & 'iend=',iend(i,iint) c do j=istart(i,iint),iend(i,iint) itypj=iabs(itype(j)) if (itypj.eq.ntyp1) cycle - xj=c(1,nres+j)-xi - yj=c(2,nres+j)-yi - zj=c(3,nres+j)-zi + xj=boxshift(c(1,nres+j)-xi,boxxsize) + yj=boxshift(c(2,nres+j)-yi,boxysize) + zj=boxshift(c(3,nres+j)-zi,boxzsize) rij=xj*xj+yj*yj+zj*zj c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj r0ij=r0(itypi,itypj) @@ -2716,7 +2523,7 @@ c include 'COMMON.CONTACTS' include 'COMMON.VECTORS' include 'COMMON.FFIELD' dimension ggg(3) - integer xshift,yshift,zshift + double precision boxshift C write(iout,*) 'In EELEC_soft_sphere' ees=0.0D0 evdw1=0.0D0 @@ -2732,12 +2539,7 @@ C write(iout,*) 'In EELEC_soft_sphere' xmedi=c(1,i)+0.5d0*dxi ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi - xmedi=mod(xmedi,boxxsize) - if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) - if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) - if (zmedi.lt.0) zmedi=zmedi+boxzsize + call to_box(xmedi,ymedi,zmedi) num_conti=0 c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) @@ -2754,43 +2556,10 @@ c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) xj=c(1,j)+0.5D0*dxj yj=c(2,j)+0.5D0*dyj zj=c(3,j)+0.5D0*dzj - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize - dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - isubchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - isubchap=1 - endif - enddo - enddo - enddo - if (isubchap.eq.1) then - xj=xj_temp-xmedi - yj=yj_temp-ymedi - zj=zj_temp-zmedi - else - xj=xj_safe-xmedi - yj=yj_safe-ymedi - zj=zj_safe-zmedi - endif + call to_box(xj,yj,zj) + xj=boxshift(xj-xmedi,boxxsize) + yj=boxshift(yj-ymedi,boxysize) + zj=boxshift(zj-zmedi,boxzsize) rij=xj*xj+yj*yj+zj*zj sss=sscale(sqrt(rij),r_cut_int) sssgrad=sscagrad(sqrt(rij),r_cut_int) @@ -3786,12 +3555,7 @@ c end if xmedi=c(1,i)+0.5d0*dxi ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi - xmedi=mod(xmedi,boxxsize) - if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) - if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) - if (zmedi.lt.0) zmedi=zmedi+boxzsize + call to_box(xmedi,ymedi,zmedi) num_conti=0 call eelecij(i,i+2,ees,evdw1,eel_loc) if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3) @@ -3846,13 +3610,7 @@ c if ((zmedi.gt.((0.5d0)*boxzsize)).or. c & (zmedi.lt.((-0.5d0)*boxzsize))) then c go to 196 c endif - xmedi=mod(xmedi,boxxsize) - if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) - if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) - if (zmedi.lt.0) zmedi=zmedi+boxzsize - + call to_box(xmedi,ymedi,zmedi) #ifdef FOURBODY num_conti=num_cont_hb(i) #endif @@ -3895,12 +3653,7 @@ c & .or. itype(i-1).eq.ntyp1 xmedi=c(1,i)+0.5d0*dxi ymedi=c(2,i)+0.5d0*dyi zmedi=c(3,i)+0.5d0*dzi - xmedi=mod(xmedi,boxxsize) - if (xmedi.lt.0) xmedi=xmedi+boxxsize - ymedi=mod(ymedi,boxysize) - if (ymedi.lt.0) ymedi=ymedi+boxysize - zmedi=mod(zmedi,boxzsize) - if (zmedi.lt.0) zmedi=zmedi+boxzsize + call to_box(xmedi,ymedi,zmedi) C xmedi=xmedi+xshift*boxxsize C ymedi=ymedi+yshift*boxysize C zmedi=zmedi+zshift*boxzsize @@ -3940,7 +3693,7 @@ c do j=ielstart(i),ielend(i) C do j=16,17 C write (iout,*) i,j C if (j.le.1) cycle - if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1 + if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds c & .or.((j+2).gt.nres) c & .or.((j-1).le.0) @@ -3948,7 +3701,7 @@ C end of changes by Ana c & .or.itype(j+2).eq.ntyp1 c & .or.itype(j-1).eq.ntyp1 &) cycle - call eelecij(i,j,ees,evdw1,eel_loc) + call eelecij(i,j,ees,evdw1,eel_loc) c enddo ! j #ifdef FOURBODY num_cont_hb(i)=num_conti @@ -4017,10 +3770,9 @@ C------------------------------------------------------------------------------- & 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 xmedi,ymedi,zmedi double precision sscale,sscagrad,scalar - + double precision boxshift c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions #ifdef MOMENT double precision scal_el /1.0d0/ @@ -4032,7 +3784,6 @@ C 13-go grudnia roku pamietnego... double precision unmat(3,3) /1.0d0,0.0d0,0.0d0, & 0.0d0,1.0d0,0.0d0, & 0.0d0,0.0d0,1.0d0/ - integer xshift,yshift,zshift c time00=MPI_Wtime() cd write (iout,*) "eelecij",i,j c ind=ind+1 @@ -4055,73 +3806,12 @@ C zj=c(3,j)+0.5D0*dzj-zmedi xj=c(1,j)+0.5D0*dxj yj=c(2,j)+0.5D0*dyj zj=c(3,j)+0.5D0*dzj - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize - if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ" - dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - isubchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - isubchap=1 - endif - enddo - enddo - enddo - if (isubchap.eq.1) then - xj=xj_temp-xmedi - yj=yj_temp-ymedi - zj=zj_temp-zmedi - else - xj=xj_safe-xmedi - yj=yj_safe-ymedi - zj=zj_safe-zmedi - endif + call to_box(xj,yj,zj) + xj=boxshift(xj-xmedi,boxxsize) + yj=boxshift(yj-ymedi,boxysize) + zj=boxshift(zj-zmedi,boxzsize) C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC c 174 continue -c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize -c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize -C Condition for being inside the proper box -c if ((xj.gt.((0.5d0)*boxxsize)).or. -c & (xj.lt.((-0.5d0)*boxxsize))) then -c go to 174 -c endif -c 175 continue -c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize -c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize -C Condition for being inside the proper box -c if ((yj.gt.((0.5d0)*boxysize)).or. -c & (yj.lt.((-0.5d0)*boxysize))) then -c go to 175 -c endif -c 176 continue -c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize -c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize -C Condition for being inside the proper box -c if ((zj.gt.((0.5d0)*boxzsize)).or. -c & (zj.lt.((-0.5d0)*boxzsize))) then -c go to 176 -c endif -C endif !endPBC condintion -C xj=xj-xmedi -C yj=yj-ymedi -C zj=zj-zmedi rij=xj*xj+yj*yj+zj*zj sss=sscale(dsqrt(rij),r_cut_int) @@ -5569,7 +5259,7 @@ C include 'COMMON.IOUNITS' include 'COMMON.CONTROL' dimension ggg(3) - integer xshift,yshift,zshift + double precision boxshift evdw2=0.0D0 evdw2_14=0.0d0 r0_scp=4.5d0 @@ -5612,12 +5302,7 @@ c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or. c & (zi.lt.((zshift-0.5d0)*boxzsize))) then c go to 136 c endif - xi=mod(xi,boxxsize) - if (xi.lt.0) xi=xi+boxxsize - yi=mod(yi,boxysize) - if (yi.lt.0) yi=yi+boxysize - zi=mod(zi,boxzsize) - if (zi.lt.0) zi=zi+boxzsize + call to_box(xi,yi,zi) C xi=xi+xshift*boxxsize C yi=yi+yshift*boxysize C zi=zi+zshift*boxzsize @@ -5634,67 +5319,10 @@ C Uncomment following three lines for Ca-p interactions xj=c(1,j) yj=c(2,j) zj=c(3,j) -c 174 continue -c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize -c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize -C Condition for being inside the proper box -c if ((xj.gt.((0.5d0)*boxxsize)).or. -c & (xj.lt.((-0.5d0)*boxxsize))) then -c go to 174 -c endif -c 175 continue -c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize -c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize -cC Condition for being inside the proper box -c if ((yj.gt.((0.5d0)*boxysize)).or. -c & (yj.lt.((-0.5d0)*boxysize))) then -c go to 175 -c endif -c 176 continue -c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize -c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize -C Condition for being inside the proper box -c if ((zj.gt.((0.5d0)*boxzsize)).or. -c & (zj.lt.((-0.5d0)*boxzsize))) then -c go to 176 - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - subchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - subchap=1 - endif - enddo - enddo - enddo - if (subchap.eq.1) then - xj=xj_temp-xi - yj=yj_temp-yi - zj=zj_temp-zi - else - xj=xj_safe-xi - yj=yj_safe-yi - zj=zj_safe-zi - endif -c c endif + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) C xj=xj-xi C yj=yj-yi C zj=zj-zi @@ -5716,32 +5344,6 @@ C ggg(1)=xj*fac ggg(2)=yj*fac ggg(3)=zj*fac -cgrad if (j.lt.i) then -cd write (iout,*) 'ji' -cgrad do k=1,3 -cgrad ggg(k)=-ggg(k) -C Uncomment following line for SC-p interactions -c gradx_scp(k,j)=gradx_scp(k,j)-ggg(k) -cgrad enddo -cgrad endif -cgrad do k=1,3 -cgrad gvdwc_scp(k,i)=gvdwc_scp(k,i)-0.5D0*ggg(k) -cgrad enddo -cgrad kstart=min0(i+1,j) -cgrad kend=max0(i-1,j-1) -cd write (iout,*) 'i=',i,' j=',j,' kstart=',kstart,' kend=',kend -cd write (iout,*) ggg(1),ggg(2),ggg(3) -cgrad do k=kstart,kend -cgrad do l=1,3 -cgrad gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l) -cgrad enddo -cgrad enddo do k=1,3 gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k) gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k) @@ -5774,15 +5376,13 @@ C include 'COMMON.IOUNITS' include 'COMMON.CONTROL' include 'COMMON.SPLITELE' - integer xshift,yshift,zshift double precision ggg(3) integer i,iint,j,k,iteli,itypj,subchap,ikont 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 + double precision boxshift evdw2=0.0D0 evdw2_14=0.0d0 c print *,boxxsize,boxysize,boxzsize,'wymiary pudla' @@ -5801,43 +5401,7 @@ c do i=iatscp_s,iatscp_e xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) zi=0.5D0*(c(3,i)+c(3,i+1)) - xi=mod(xi,boxxsize) - if (xi.lt.0) xi=xi+boxxsize - yi=mod(yi,boxysize) - if (yi.lt.0) yi=yi+boxysize - zi=mod(zi,boxzsize) - if (zi.lt.0) zi=zi+boxzsize -c xi=xi+xshift*boxxsize -c yi=yi+yshift*boxysize -c zi=zi+zshift*boxzsize -c print *,xi,yi,zi,'polozenie i' -C Return atom into box, boxxsize is size of box in x dimension -c 134 continue -c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize -c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize -C Condition for being inside the proper box -c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or. -c & (xi.lt.((xshift-0.5d0)*boxxsize))) then -c go to 134 -c endif -c 135 continue -c print *,xi,boxxsize,"pierwszy" - -c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize -c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize -C Condition for being inside the proper box -c if ((yi.gt.((yshift+0.5d0)*boxysize)).or. -c & (yi.lt.((yshift-0.5d0)*boxysize))) then -c go to 135 -c endif -c 136 continue -c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize -c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize -C Condition for being inside the proper box -c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or. -c & (zi.lt.((zshift-0.5d0)*boxzsize))) then -c go to 136 -c endif + call to_box(xi,yi,zi) c do iint=1,nscp_gr(i) c do j=iscpstart(i,iint),iscpend(i,iint) @@ -5851,68 +5415,10 @@ C Uncomment following three lines for Ca-p interactions xj=c(1,j) yj=c(2,j) zj=c(3,j) - xj=mod(xj,boxxsize) - if (xj.lt.0) xj=xj+boxxsize - yj=mod(yj,boxysize) - if (yj.lt.0) yj=yj+boxysize - zj=mod(zj,boxzsize) - if (zj.lt.0) zj=zj+boxzsize -c 174 continue -c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize -c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize -C Condition for being inside the proper box -c if ((xj.gt.((0.5d0)*boxxsize)).or. -c & (xj.lt.((-0.5d0)*boxxsize))) then -c go to 174 -c endif -c 175 continue -c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize -c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize -cC Condition for being inside the proper box -c if ((yj.gt.((0.5d0)*boxysize)).or. -c & (yj.lt.((-0.5d0)*boxysize))) then -c go to 175 -c endif -c 176 continue -c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize -c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize -C Condition for being inside the proper box -c if ((zj.gt.((0.5d0)*boxzsize)).or. -c & (zj.lt.((-0.5d0)*boxzsize))) then -c go to 176 -c endif -CHERE IS THE CALCULATION WHICH MIRROR IMAGE IS THE CLOSEST ONE - dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - xj_safe=xj - yj_safe=yj - zj_safe=zj - subchap=0 - do xshift=-1,1 - do yshift=-1,1 - do zshift=-1,1 - xj=xj_safe+xshift*boxxsize - yj=yj_safe+yshift*boxysize - zj=zj_safe+zshift*boxzsize - dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 - if(dist_temp.lt.dist_init) then - dist_init=dist_temp - xj_temp=xj - yj_temp=yj - zj_temp=zj - subchap=1 - endif - enddo - enddo - enddo - if (subchap.eq.1) then - xj=xj_temp-xi - yj=yj_temp-yi - zj=zj_temp-zi - else - xj=xj_safe-xi - yj=yj_safe-yi - zj=zj_safe-zi - endif + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) c print *,xj,yj,zj,'polozenie j' rrij=1.0D0/(xj*xj+yj*yj+zj*zj) c print *,rrij @@ -13638,3 +13144,103 @@ C----------------------------------------------------------------------- endif return end +c------------------------------------------------------------------------ + double precision function boxshift(x,boxsize) + implicit none + double precision x,boxsize + double precision xtemp + xtemp=dmod(x,boxsize) + if (dabs(xtemp-boxsize).lt.dabs(xtemp)) then + boxshift=xtemp-boxsize + else if (dabs(xtemp+boxsize).lt.dabs(xtemp)) then + boxshift=xtemp+boxsize + else + boxshift=xtemp + endif + return + end +c-------------------------------------------------------------------------- + subroutine closest_img(xi,yi,zi,xj,yj,zj) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + integer xshift,yshift,zshift,subchap + double precision dist_init,xj_safe,yj_safe,zj_safe, + & xj_temp,yj_temp,zj_temp,dist_temp + xj_safe=xj + yj_safe=yj + zj_safe=zj + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + return + end +c-------------------------------------------------------------------------- + subroutine to_box(xi,yi,zi) + implicit none + include 'DIMENSIONS' + include 'COMMON.CHAIN' + double precision xi,yi,zi + xi=dmod(xi,boxxsize) + if (xi.lt.0.0d0) xi=xi+boxxsize + yi=dmod(yi,boxysize) + if (yi.lt.0.0d0) yi=yi+boxysize + zi=dmod(zi,boxzsize) + if (zi.lt.0.0d0) zi=zi+boxzsize + return + end +c-------------------------------------------------------------------------- + subroutine lipid_layer(xi,yi,zi,sslipi,ssgradlipi) + implicit none + include 'DIMENSIONS' + include 'COMMON.CHAIN' + double precision xi,yi,zi,sslipi,ssgradlipi + double precision fracinbuf + double precision sscalelip,sscagradlip + + if ((zi.gt.bordlipbot).and.(zi.lt.bordliptop)) then +C the energy transfer exist + if (zi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0-((zi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif + return + end