X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fenergy_p_new_barrier.F;h=9271240aaff989920105157fb8a10df0578752c8;hb=d7d33ac73e7386cf74bb07da09b67fa6619a0b11;hp=7207b35c4f2b5075be6cefe490c0accd9508166f;hpb=0c5fb524ca994d617a32adfb678302e2f3dcef1e;p=unres.git diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F index 7207b35..9271240 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -99,6 +99,7 @@ c endif C C Compute the side-chain and electrostatic interaction energy C +C print *,ipot goto (101,102,103,104,105,106) ipot C Lennard-Jones potential. 101 call elj(evdw) @@ -112,6 +113,7 @@ C Berne-Pechukas potential (dilated LJ, angular dependence). goto 107 C Gay-Berne potential (shifted LJ, angular dependence). 104 call egb(evdw) +C print *,"bylem w egb" goto 107 C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence). 105 call egbv(evdw) @@ -455,8 +457,9 @@ cMS$ATTRIBUTES C :: proc_proc #ifdef MPI include 'mpif.h' #endif - double precision gradbufc(3,0:maxres),gradbufx(3,0:maxres), - & glocbuf(4*maxres),gradbufc_sum(3,0:maxres),gloc_scbuf(3,0:maxres) + double precision gradbufc(3,-1:maxres),gradbufx(3,-1:maxres), + & glocbuf(4*maxres),gradbufc_sum(3,-1:maxres) + & ,gloc_scbuf(3,-1:maxres) include 'COMMON.SETUP' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' @@ -509,7 +512,7 @@ c enddo call flush(iout) #endif #ifdef SPLITELE - do i=1,nct + do i=0,nct do j=1,3 gradbufc(j,i)=wsc*gvdwc(j,i)+ & wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+ @@ -525,7 +528,7 @@ c enddo enddo enddo #else - do i=1,nct + do i=0,nct do j=1,3 gradbufc(j,i)=wsc*gvdwc(j,i)+ & wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+ @@ -551,7 +554,7 @@ c enddo enddo call flush(iout) #endif - do i=1,nres + do i=0,nres do j=1,3 gradbufc_sum(j,i)=gradbufc(j,i) enddo @@ -594,7 +597,7 @@ c enddo do j=1,3 gradbufc(j,nres-1)=gradbufc_sum(j,nres) enddo - do i=nres-2,nnt,-1 + do i=nres-2,-1,-1 do j=1,3 gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1) enddo @@ -615,7 +618,7 @@ c enddo enddo call flush(iout) #endif - do i=1,nres + do i=-1,nres do j=1,3 gradbufc_sum(j,i)=gradbufc(j,i) gradbufc(j,i)=0.0d0 @@ -624,7 +627,7 @@ c enddo do j=1,3 gradbufc(j,nres-1)=gradbufc_sum(j,nres) enddo - do i=nres-2,nnt,-1 + do i=nres-2,-1,-1 do j=1,3 gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1) enddo @@ -652,7 +655,7 @@ c enddo do k=1,3 gradbufc(k,nres)=0.0d0 enddo - do i=1,nct + do i=-1,nct do j=1,3 #ifdef SPLITELE gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ @@ -1110,13 +1113,13 @@ c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj eps0ij=eps(itypi,itypj) fac=rrij**expon2 C have you changed here? - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e1+e2 cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj) cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)') -cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), +cd & restyp(itypi),i,restyp(itypj),j,a(itypi,itypj), cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) evdw=evdw+evdwij @@ -1261,8 +1264,8 @@ C r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj)) fac=r_shift_inv**expon C have you changed here? - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e_augm+e1+e2 cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj) @@ -1390,16 +1393,16 @@ C Calculate whole angle-dependent part of epsilon and contributions C to its derivatives C have you changed here? fac=(rrij*sigsq)**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt evdwij=evdwij*eps2rt*eps3rt evdw=evdw+evdwij if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + sigm=dabs(aa/bb)**(1.0D0/6.0D0) + epsi=bb**2/aa cd write (iout,'(2(a3,i3,2x),15(0pf7.3))') cd & restyp(itypi),i,restyp(itypj),j, cd & epsi,sigm,chi1,chi2,chip1,chip2, @@ -1449,7 +1452,7 @@ C integer xshift,yshift,zshift evdw=0.0D0 ccccc energy_dec=.false. -c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon +C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 lprn=.false. c if (icall.eq.0) lprn=.false. @@ -1497,6 +1500,35 @@ c endif if (yi.lt.0) yi=yi+boxysize zi=mod(zi,boxzsize) if (zi.lt.0) zi=zi+boxzsize +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 + C xi=xi+xshift*boxxsize C yi=yi+yshift*boxysize C zi=zi+zshift*boxzsize @@ -1581,6 +1613,36 @@ c endif 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 (zi.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 + if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)') + &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) +C if (ssgradlipj.gt.0.0d0) print *,"??WTF??" + print *,sslipi,sslipj,bordlipbot,zi,zj dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 xj_safe=xj yj_safe=yj @@ -1651,18 +1713,22 @@ c--------------------------------------------------------------- fac=rij_shift**expon C here to start with C if (c(i,3).gt. - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + 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(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + 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, @@ -1684,6 +1750,14 @@ c & evdwij,fac,sigma(itypi,itypj),expon fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*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 +C gg_lipi(3)=0.0d0 +C gg_lipj(3)=0.0d0 gg(1)=xj*fac gg(2)=yj*fac gg(3)=zj*fac @@ -1733,6 +1807,41 @@ c if (icall.eq.0) lprn=.true. 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 +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- + & ((positi-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-positi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif + dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -1769,9 +1878,74 @@ 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 +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- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-positi)/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 +C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5') +C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj)) + 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) @@ -1792,8 +1966,8 @@ C I hate to put IF's in the loops, but here don't have another choice!!!! c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=eps1*eps2rt*eps3rt*(e1+e2) eps2der=evdwij*eps3rt eps3der=evdwij*eps2rt @@ -1802,8 +1976,8 @@ c--------------------------------------------------------------- evdwij=evdwij*eps2rt*eps3rt evdw=evdw+evdwij+e_augm if (lprn) then - sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) - epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + 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), @@ -1817,6 +1991,7 @@ C Calculate gradient components. fac=-expon*(e1+evdwij)*rij_shift sigder=fac*sigder fac=rij*fac-2*expon*rrij*e_augm + fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij C Calculate the radial part of the gradient gg(1)=xj*fac gg(2)=yj*fac @@ -1927,10 +2102,10 @@ c write (iout,*) "eom1",eom1," eom2",eom2," eom12",eom12 enddo c write (iout,*) "gg",(gg(k),k=1,3) do k=1,3 - gvdwx(k,i)=gvdwx(k,i)-gg(k) + gvdwx(k,i)=gvdwx(k,i)-gg(k)+gg_lipi(k) & +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss - gvdwx(k,j)=gvdwx(k,j)+gg(k) + gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k) & +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss c write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) @@ -1947,8 +2122,8 @@ cgrad gvdwc(l,k)=gvdwc(l,k)+gg(l) cgrad enddo cgrad enddo do l=1,3 - gvdwc(l,i)=gvdwc(l,i)-gg(l) - gvdwc(l,j)=gvdwc(l,j)+gg(l) + gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(l) + gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(l) enddo return end @@ -9708,6 +9883,7 @@ CCC---------------------------------------------- include 'COMMON.CONTROL' include 'COMMON.SPLITELE' include 'COMMON.SBRIDGE' +C this is done by Adasko C print *,"wchodze" C structure of box: C water @@ -9718,9 +9894,10 @@ C--buflipbot--- lipid ends buffore starts C--bordlipbot--buffore ends eliptran=0.0 do i=ilip_start,ilip_end +C do i=1,1 if (itype(i).eq.ntyp1) cycle - positi=(mod((c(3,i)+c(3,i+1)),boxzsize)) + positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize)) if (positi.le.0) positi=positi+boxzsize C print *,i C first for peptide groups @@ -9736,8 +9913,8 @@ C lipbufthick is thickenes of lipid buffore sslip=sscalelip(fracinbuf) ssgradlip=-sscagradlip(fracinbuf)/lipbufthick eliptran=eliptran+sslip*pepliptran - gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0 - gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0 + gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran C print *,"doing sccale for lower part" @@ -9749,10 +9926,10 @@ C print *,"doing sccale for lower part" gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0 gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran - print *, "doing sscalefor top part" +C print *, "doing sscalefor top part" else eliptran=eliptran+pepliptran - print *,"I am in true lipid" +C print *,"I am in true lipid" endif C else C eliptran=elpitran+0.0 ! I am in water @@ -9762,6 +9939,7 @@ C print *, "nic nie bylo w lipidzie?" C now multiply all by the peptide group transfer factor C eliptran=eliptran*pepliptran C now the same for side chains +C do i=1,1 do i=ilip_start,ilip_end if (itype(i).eq.ntyp1) cycle positi=(mod(c(3,i+nres),boxzsize)) @@ -9769,6 +9947,7 @@ C now the same for side chains C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop c for each residue check if it is in lipid or lipid water border area C respos=mod(c(3,i+nres),boxzsize) +C print *,positi,bordlipbot,buflipbot if ((positi.gt.bordlipbot) & .and.(positi.lt.bordliptop)) then C the energy transfer exist @@ -9781,9 +9960,9 @@ C lipbufthick is thickenes of lipid buffore eliptran=eliptran+sslip*liptranene(itype(i)) gliptranx(3,i)=gliptranx(3,i) &+ssgradlip*liptranene(itype(i))/2.0d0 - gliptranc(3,i-1)= - &+ssgradlip*liptranene(itype(i)) - print *,"doing sccale for lower part" + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i))/2.0d0 +C print *,"doing sccale for lower part" elseif (positi.gt.bufliptop) then fracinbuf=1.0d0- &((bordliptop-positi)/lipbufthick) @@ -9792,12 +9971,12 @@ C lipbufthick is thickenes of lipid buffore eliptran=eliptran+sslip*liptranene(itype(i)) gliptranx(3,i)=gliptranx(3,i) &+ssgradlip*liptranene(itype(i))/2.0d0 - gliptranc(3,i-1)= - &+ssgradlip*liptranene(itype(i)) - print *, "doing sscalefor top part",sslip,fracinbuf + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i))/2.0d0 +C print *, "doing sscalefor top part",sslip,fracinbuf else eliptran=eliptran+liptranene(itype(i)) - print *,"I am in true lipid" +C print *,"I am in true lipid" endif endif ! if in lipid or buffor C else