X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=cba6b5e3c1a1ca116c5c77ce4237a86b04b82a7f;hp=a7b07987ebba738b947d71905a22d3cdacf914a2;hb=25618f9f83673a7063414fe1e17415d138f58da8;hpb=3444e732000b8e1ae809ef2fab7a828697a9eb78 diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F index a7b0798..cba6b5e 100644 --- a/source/wham/src-M/energy_p_new.F +++ b/source/wham/src-M/energy_p_new.F @@ -91,6 +91,11 @@ C C 21/5/07 Calculate local sicdechain correlation energy C call eback_sc_corr(esccor) + + if (wliptran.gt.0) then + call Eliptransfer(eliptran) + endif + C C 12/1/95 Multi-body terms C @@ -116,6 +121,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t & +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 #else etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2 & +welec*fact(1)*(ees+evdw1) @@ -125,6 +131,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t & +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 #endif energia(0)=etot energia(1)=evdw @@ -159,6 +166,7 @@ c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t energia(20)=edihcnstr energia(21)=evdw_t energia(24)=ethetacnstr + energia(22)=eliptran c detecting NaNQ #ifdef ISNAN #ifdef AIX @@ -197,10 +205,12 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(2)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) enddo #else do i=1,nct @@ -216,10 +226,12 @@ C & wcorr6*fact(5)*gradcorr6(j,i)+ & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) + & +wliptran*gliptranc(j,i) gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(1)*gsccorx(j,i) + & +wliptran*gliptranx(j,i) enddo #endif enddo @@ -276,6 +288,7 @@ C------------------------------------------------------------------------ edihcnstr=energia(20) estr=energia(18) ethetacnstr=energia(24) + eliptran=energia(22) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1, & wvdwpp, @@ -284,7 +297,8 @@ C------------------------------------------------------------------------ & 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,ethetacnstr,ebr*nss,etot + & esccor,wsccor*fact(1),edihcnstr,ethetacnstr,ebr*nss, + & eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -308,6 +322,7 @@ C------------------------------------------------------------------------ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond, @@ -316,7 +331,7 @@ C------------------------------------------------------------------------ & 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,ethetacnstr,ebr*nss,etot + & edihcnstr,ethetacnstr,ebr*nss,eliptran,wliptran,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -339,6 +354,7 @@ C------------------------------------------------------------------------ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -407,8 +423,8 @@ C Change 12/1/95 to calculate four-body interactions c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj eps0ij=eps(itypi,itypj) fac=rrij**expon2 - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e1+e2 ij=icant(itypi,itypj) c ROZNICA z cluster @@ -422,7 +438,7 @@ 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 & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -580,8 +596,8 @@ C rij=1.0D0/r_inv_ij r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj)) fac=r_shift_inv**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) + e1=fac*fac*aa + e2=fac*bb evdwij=e_augm+e1+e2 ij=icant(itypi,itypj) eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm) @@ -594,7 +610,7 @@ cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, cd & (c(k,i),k=1,3),(c(k,j),k=1,3) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij @@ -726,8 +742,8 @@ C Calculate the angle-dependent terms of energy & contributions to derivatives. C Calculate whole angle-dependent part of epsilon and contributions C to its derivatives 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 @@ -737,15 +753,15 @@ C to its derivatives eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux & /dabs(eps(itypi,itypj)) eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj) - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij else evdw_t=evdw_t+evdwij endif if (calc_grad) then 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),15(0pf7.3))') & restyp(itypi),i,restyp(itypj),j, & epsi,sigm,chi1,chi2,chip1,chip2, @@ -822,6 +838,28 @@ C returning the ith atom to box if (yi.lt.0) yi=yi+boxysize zi=mod(zi,boxzsize) if (zi.lt.0) zi=zi+boxzsize + 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 dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) @@ -886,6 +924,33 @@ C returning jth atom to box 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 +C write(iout,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj) C checking the distance dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 xj_safe=xj @@ -931,6 +996,7 @@ c write (iout,*) i,j,xj,yj,zj if (sss.le.0.0) cycle C Calculate angle-dependent terms of energy and contributions to their C derivatives. + call sc_angular sigsq=1.0D0/sigsq sig=sig0ij*dsqrt(sigsq) @@ -944,13 +1010,13 @@ 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 evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0) then + if (bb.gt.0) then evdw=evdw+evdwij*sss else evdw_t=evdw_t+evdwij*sss @@ -964,8 +1030,8 @@ 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 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 #ifdef DEBUG write (iout,'(2(a3,i3,2x),17(0pf7.3))') & restyp(itypi),i,restyp(itypj),j, @@ -1097,15 +1163,15 @@ 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 fac_augm=rrij**expon e_augm=augm(itypi,itypj)*fac_augm evdwij=evdwij*eps2rt*eps3rt - if (bb(itypi,itypj).gt.0.0d0) then + if (bb.gt.0.0d0) then evdw=evdw+evdwij+e_augm else evdw_t=evdw_t+evdwij+e_augm @@ -1816,6 +1882,8 @@ c print *,"itilde3 i iti iti1",i,iti,iti1 do k=1,2 mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1) enddo +C write (iout,*) 'mumu',i,b1(1,iti),Ub2(1,i-2) + C Vectors and matrices dependent on a single virtual-bond dihedral. call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1)) call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2)) @@ -2437,8 +2505,9 @@ C Contribution to the local-electrostatic energy coming from the i-j pair eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3) & +a33*muij(4) c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij -c write (iout,'(a6,2i5,0pf7.3)') -c & 'eelloc',i,j,eel_loc_ij +C write (iout,'(a6,2i5,0pf7.3)') +C & 'eelloc',i,j,eel_loc_ij +C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4) c write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3) eel_loc=eel_loc+eel_loc_ij C Partial derivatives in virtual-bond dihedral angles gamma @@ -2776,6 +2845,16 @@ C Cartesian derivatives enddo endif else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then + if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds + & .or.((i+5).gt.nres) + & .or.((i-1).le.0) +C end of changes suggested by Ana + & .or. itype(i+3).eq.ntyp1 + & .or. itype(i+4).eq.ntyp1 + & .or. itype(i+5).eq.ntyp1 + & .or. itype(i).eq.ntyp1 + & .or. itype(i-1).eq.ntyp1) goto 178 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C Fourth-order contributions @@ -2915,6 +2994,7 @@ C Remaining derivatives of this turn contribution gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) enddo endif + 178 continue endif return end @@ -7774,6 +7854,125 @@ cd write (2,*) 'eel_turn6',ekont*eel_turn6 return end crc------------------------------------------------- +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + subroutine Eliptransfer(eliptran) + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.GEO' + include 'COMMON.VAR' + include 'COMMON.LOCAL' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' +C this is done by Adasko +C print *,"wchodze" +C structure of box: +C water +C--bordliptop-- buffore starts +C--bufliptop--- here true lipid starts +C lipid +C--buflipbot--- lipid ends buffore starts +C--bordlipbot--buffore ends + eliptran=0.0 + do i=1,nres +C do i=1,1 + if (itype(i).eq.ntyp1) cycle + + 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 +c for each residue check if it is in lipid or lipid water border area + if ((positi.gt.bordlipbot) + &.and.(positi.lt.bordliptop)) then +C the energy transfer exist + if (positi.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +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/2.0d0 + gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0 +C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*pepliptran + 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 sscalefor top part" +C print *,i,sslip,fracinbuf,ssgradlip + else + eliptran=eliptran+pepliptran +C print *,"I am in true lipid" + endif +C else +C eliptran=elpitran+0.0 ! I am in water + endif + enddo +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 +CV do i=1,1 + do i=1,nres + if (itype(i).eq.ntyp1) cycle + positi=(mod(c(3,i+nres),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +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 + if (positi.lt.buflipbot) then + fracinbuf=1.0d0- + & ((positi-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslip=sscalelip(fracinbuf) + ssgradlip=-sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *,"doing sccale for lower part" + elseif (positi.gt.bufliptop) then + fracinbuf=1.0d0- + &((bordliptop-positi)/lipbufthick) + sslip=sscalelip(fracinbuf) + ssgradlip=sscagradlip(fracinbuf)/lipbufthick + eliptran=eliptran+sslip*liptranene(itype(i)) + gliptranx(3,i)=gliptranx(3,i) + &+ssgradlip*liptranene(itype(i)) + gliptranc(3,i-1)= gliptranc(3,i-1) + &+ssgradlip*liptranene(itype(i)) +C print *, "doing sscalefor top part",sslip,fracinbuf + else + eliptran=eliptran+liptranene(itype(i)) +C print *,"I am in true lipid" + endif + endif ! if in lipid or buffor +C else +C eliptran=elpitran+0.0 ! I am in water + enddo + return + end + + +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + SUBROUTINE MATVEC2(A1,V1,V2) implicit real*8 (a-h,o-z) include 'DIMENSIONS' @@ -7937,4 +8136,34 @@ C----------------------------------------------------------------------- return end C----------------------------------------------------------------------- +C----------------------------------------------------------------------- + double precision function sscalelip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscale=1.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscalelip=1.0d0+r*r*(2*r-3.0d0) +C else +C sscale=0d0 +C endif + return + end +C----------------------------------------------------------------------- + double precision function sscagradlip(r) + double precision r,gamm + include "COMMON.SPLITELE" +C if(r.lt.r_cut-rlamb) then +C sscagrad=0.0d0 +C else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then +C gamm=(r-(r_cut-rlamb))/rlamb + sscagradlip=r*(6*r-6.0d0) +C else +C sscagrad=0.0d0 +C endif + return + end + +C-----------------------------------------------------------------------