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=109af351c026cf52a7ab4975e320166eb0a54e1d;hb=7ac044004baeac41c3c91c38a1b3c3546287e624;hp=af14adb6df0e6a6cfd2f8043f7241e2a57d6bd15;hpb=dea2e7e9c8a159fba253863186d91d90930f17c6;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 af14adb..109af35 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) @@ -135,6 +137,14 @@ c print *,"Processor",myrank," computed USCSC" #ifdef TIMING time_vec=time_vec+MPI_Wtime()-time01 #endif +C Introduction of shielding effect first for each peptide group +C the shielding factor is set this factor is describing how each +C peptide group is shielded by side-chains +C the matrix - shield_fac(i) the i index describe the ith between i and i+1 + write (iout,*) "shield_mode",shield_mode + if (shield_mode.gt.0) then + call set_shield_fac + endif c print *,"Processor",myrank," left VEC_AND_DERIV" if (ipot.lt.6) then #ifdef SPLITELE @@ -191,14 +201,16 @@ C C Calculate the virtual-bond-angle energy. C if (wang.gt.0d0) then - call ebend(ebe) + call ebend(ebe,ethetacnstr) else ebe=0 + ethetacnstr=0 endif c print *,"Processor",myrank," computed UB" C C Calculate the SC local energy. C +C print *,"TU DOCHODZE?" call esc(escloc) c print *,"Processor",myrank," computed USC" C @@ -229,6 +241,7 @@ C else esccor=0.0d0 endif +C print *,"PRZED MULIt" c print *,"Processor",myrank," computed Usccorr" C C 12/1/95 Multi-body terms @@ -261,6 +274,19 @@ C after the equilibration time Uconst=0.0d0 Uconst_back=0.0d0 endif +C 01/27/2015 added by adasko +C the energy component below is energy transfer into lipid environment +C based on partition function +C print *,"przed lipidami" + if (wliptran.gt.0) then + call Eliptransfer(eliptran) + endif +C print *,"za lipidami" + if (AFMlog.gt.0) then + call AFMforce(Eafmforce) + else if (selfguide.gt.0) then + call AFMvel(Eafmforce) + endif #ifdef TIMING time_enecalc=time_enecalc+MPI_Wtime()-time00 #endif @@ -302,6 +328,9 @@ C energia(17)=estr energia(20)=Uconst+Uconst_back energia(21)=esccor + energia(22)=eliptran + energia(23)=Eafmforce + energia(24)=ethetacnstr c Here are the energies showed per procesor if the are more processors c per molecule then we sum it up in sum_energy subroutine c print *," Processor",myrank," calls SUM_ENERGY" @@ -393,20 +422,26 @@ cMS$ATTRIBUTES C :: proc_proc estr=energia(17) Uconst=energia(20) esccor=energia(21) + eliptran=energia(22) + Eafmforce=energia(23) + ethetacnstr=energia(24) #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d - & +wbond*estr+Uconst+wsccor*esccor + & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce + & +ethetacnstr #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d - & +wbond*estr+Uconst+wsccor*esccor + & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran + & +Eafmforce + & +ethetacnstr #endif energia(0)=etot c detecting NaNQ @@ -443,8 +478,9 @@ cMS$ATTRIBUTES C :: proc_proc #ifdef MPI include 'mpif.h' #endif - double precision gradbufc(3,maxres),gradbufx(3,maxres), - & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,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' @@ -497,7 +533,7 @@ 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))+ @@ -508,10 +544,13 @@ c enddo & wcorr6*gradcorr6_long(j,i)+ & wturn6*gcorr6_turn_long(j,i)+ & wstrain*ghpbc(j,i) + & +wliptran*gliptranc(j,i) + & +gradafm(j,i) + 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))+ @@ -523,6 +562,9 @@ c enddo & wcorr6*gradcorr6_long(j,i)+ & wturn6*gcorr6_turn_long(j,i)+ & wstrain*ghpbc(j,i) + & +wliptran*gliptranc(j,i) + & +gradafm(j,i) + enddo enddo #endif @@ -536,7 +578,7 @@ 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 @@ -579,7 +621,7 @@ 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 @@ -600,7 +642,7 @@ 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 @@ -609,7 +651,7 @@ 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 @@ -637,7 +679,7 @@ 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)+ @@ -658,6 +700,8 @@ c enddo & wturn6*gcorr6_turn(j,i)+ & wsccor*gsccorc(j,i) & +wscloc*gscloc(j,i) + & +wliptran*gliptranc(j,i) + & +gradafm(j,i) #else gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ & wel_loc*gel_loc(j,i)+ @@ -677,12 +721,16 @@ c enddo & wturn6*gcorr6_turn(j,i)+ & wsccor*gsccorc(j,i) & +wscloc*gscloc(j,i) + & +wliptran*gliptranc(j,i) + & +gradafm(j,i) + #endif 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*gsccorx(j,i) & +wscloc*gsclocx(j,i) + & +wliptran*gliptranx(j,i) enddo enddo #ifdef DEBUG @@ -971,15 +1019,18 @@ C------------------------------------------------------------------------ estr=energia(17) Uconst=energia(20) esccor=energia(21) + eliptran=energia(22) + Eafmforce=energia(23) + ethetacnstr=energia(24) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp, & estr,wbond,ebe,wang, & escloc,wscloc,etors,wtor,etors_d,wtor_d,ehpb,wstrain, & ecorr,wcorr, & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3, - & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor, - & edihcnstr,ebr*nss, - & Uconst,etot + & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr, + & ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, + & etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -1001,9 +1052,13 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ + & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ & 'ETOT= ',1pE16.6,' (total)') + #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec, & estr,wbond,ebe,wang, @@ -1011,7 +1066,8 @@ C------------------------------------------------------------------------ & ecorr,wcorr, & ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3, & eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccro,edihcnstr, - & ebr*nss,Uconst,etot + & ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, + & etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ @@ -1032,8 +1088,11 @@ C------------------------------------------------------------------------ & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ + & 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST=',1pE16.6,' (Constraint energy)'/ + & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ + & 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -1088,13 +1147,14 @@ 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) +C have you changed here? + 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 @@ -1238,8 +1298,9 @@ 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) +C have you changed here? + 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) @@ -1365,17 +1426,18 @@ C Calculate the angle-dependent terms of energy & contributions to derivatives. call sc_angular 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, @@ -1423,9 +1485,10 @@ C include 'COMMON.SBRIDGE' logical lprn 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. @@ -1473,6 +1536,35 @@ 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 @@ -1490,10 +1582,36 @@ C do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN + +c write(iout,*) "PRZED ZWYKLE", evdwij call dyn_ssbond_ene(i,j,evdwij) +c write(iout,*) "PO ZWYKLE", evdwij + evdw=evdw+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) +C search over all next residues + 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) +c if(evdwij_przed_tri.ne.evdwij) then +c write (iout,*) "TRI:", evdwij, evdwij_przed_tri +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',i,j,evdwij,'tss' + endif!dyn_ss_mask(k) + enddo! k ELSE ind=ind+1 itypj=iabs(itype(j)) @@ -1557,6 +1675,36 @@ 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 (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 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 @@ -1625,18 +1773,24 @@ cd & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) c--------------------------------------------------------------- rij_shift=1.0D0/rij_shift fac=rij_shift**expon - e1=fac*fac*aa(itypi,itypj) - e2=fac*bb(itypi,itypj) +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 +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, @@ -1658,12 +1812,20 @@ 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 C Calculate angular part of the gradient. call sc_grad - endif ! sss + endif ENDIF ! dyn_ss enddo ! j enddo ! iint @@ -1707,6 +1869,41 @@ 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- + & ((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) dzi=dc_norm(3,nres+i) @@ -1743,9 +1940,74 @@ 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- + & ((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 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) @@ -1766,8 +2028,8 @@ 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 @@ -1776,8 +2038,8 @@ 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), @@ -1791,6 +2053,7 @@ 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 @@ -1901,10 +2164,10 @@ 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)) @@ -1921,8 +2184,8 @@ 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 @@ -3063,12 +3326,21 @@ C Loop over i,i+2 and i,i+3 pairs of the peptide groups C C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition do i=iturn3_start,iturn3_end + if (i.le.1) cycle +C write(iout,*) "tu jest i",i if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds + & .or.((i+4).gt.nres) + & .or.((i-1).le.0) +C end of changes by Ana & .or. itype(i+2).eq.ntyp1 - & .or. itype(i+3).eq.ntyp1 - & .or. itype(i-1).eq.ntyp1 - & .or. itype(i+4).eq.ntyp1 - & ) cycle + & .or. itype(i+3).eq.ntyp1) cycle + if(i.gt.1)then + if(itype(i-1).eq.ntyp1)cycle + end if + if(i.LT.nres-3)then + if (itype(i+4).eq.ntyp1) cycle + end if dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -3090,7 +3362,12 @@ C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition num_cont_hb(i)=num_conti enddo do i=iturn4_start,iturn4_end + if (i.le.1) cycle 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 @@ -3153,7 +3430,12 @@ c c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 c do i=iatel_s,iatel_e + if (i.le.1) cycle if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds + & .or.((i+2).gt.nres) + & .or.((i-1).le.0) +C end of changes by Ana & .or. itype(i+2).eq.ntyp1 & .or. itype(i-1).eq.ntyp1 & ) cycle @@ -3205,8 +3487,13 @@ c endif c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) num_conti=num_cont_hb(i) do j=ielstart(i),ielend(i) -c write (iout,*) i,j,itype(i),itype(j) +C write (iout,*) i,j + if (j.le.1) cycle if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1 +C changes suggested by Ana to avoid out of bounds + & .or.((j+2).gt.nres) + & .or.((j-1).le.0) +C end of changes by Ana & .or.itype(j+2).eq.ntyp1 & .or.itype(j-1).eq.ntyp1 &) cycle @@ -3249,6 +3536,7 @@ C------------------------------------------------------------------------------- include 'COMMON.FFIELD' include 'COMMON.TIME1' include 'COMMON.SPLITELE' + include 'COMMON.SHIELD' 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), @@ -3384,7 +3672,11 @@ C MARYSIA eesij=(el1+el2) C 12/26/95 - for the evaluation of multi-body H-bonding interactions ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg) + if (shield_mode.gt.0) then + ees=ees+eesij*fac_shield(i)*fac_shield(j) + else ees=ees+eesij + endif evdw1=evdw1+evdwij*sss cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)') cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i, @@ -4866,8 +5158,13 @@ C include 'COMMON.VAR' include 'COMMON.INTERACT' include 'COMMON.IOUNITS' + include 'COMMON.CONTROL' dimension ggg(3) ehpb=0.0D0 + do i=1,3 + ggg(i)=0.0d0 + enddo +C write (iout,*) ,"link_end",link_end,constr_dist cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr cd write(iout,*)'link_start=',link_start,' link_end=',link_end if (link_end.eq.0) return @@ -4888,33 +5185,90 @@ 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 (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. - & iabs(itype(jjj)).eq.1) then +C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. +C & iabs(itype(jjj)).eq.1) then cmc if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds 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 + if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. + & iabs(itype(jjj)).eq.1) then call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij endif cd write (iout,*) "eij",eij +cd & ' waga=',waga,' fac=',fac + else if (ii.gt.nres .and. jj.gt.nres) then +c Restraints from contact prediction + dd=dist(ii,jj) + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + if (energy_dec) write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, + & ehpb,fordepth(i),dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "beta nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + dd=dist(ii,jj) + rdis=dd-dhpb(i) +C Get the force constant corresponding to this distance. + waga=forcon(i) +C Calculate the contribution to energy. + ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "beta reg",dd,waga*rdis*rdis +C +C Evaluate gradient. +C + fac=waga*rdis/dd + endif + endif + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo + do j=1,3 + ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) + ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) + enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo else C Calculate the distance between the two points and its difference from the C target distance. dd=dist(ii,jj) + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)**4.0d0 + & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 + & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + if (energy_dec) write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, + & ehpb,fordepth(i),dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +c write (iout,*) "alph nmr", +c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else rdis=dd-dhpb(i) C Get the force constant corresponding to this distance. waga=forcon(i) C Calculate the contribution to energy. ehpb=ehpb+waga*rdis*rdis +c write (iout,*) "alpha reg",dd,waga*rdis*rdis C C Evaluate gradient. C fac=waga*rdis/dd -cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, -cd & ' waga=',waga,' fac=',fac + endif + endif do j=1,3 ggg(j)=fac*(c(j,jj)-c(j,ii)) enddo @@ -4937,9 +5291,8 @@ cgrad enddo ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) enddo endif - endif enddo - ehpb=0.5D0*ehpb + if (constr_dist.ne.11) ehpb=0.5D0*ehpb return end C-------------------------------------------------------------------------- @@ -5130,7 +5483,7 @@ c end #ifdef CRYST_THETA C-------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) C C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral C angles gamma and its derivatives in consecutive thetas and gammas. @@ -5147,6 +5500,7 @@ C include 'COMMON.NAMES' include 'COMMON.FFIELD' include 'COMMON.CONTROL' + include 'COMMON.TORCNSTR' common /calcthet/ term1,term2,termm,diffak,ratak, & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq, & delthe0,sig0inv,sigtc,sigsqtc,delthec,it @@ -5258,6 +5612,34 @@ C Derivatives of the "mean" values in gamma1 and gamma2. if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2 gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)+gloc(nphi+i-2,icg) enddo + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=ithetaconstr_start,ithetaconstr_end + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetcnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetcnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", + & i,itheta,rad2deg*thetiii, + & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), + & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, + & gloc(itheta+nphi-2,icg) + endif + enddo + C Ufff.... We've done all this!!! return end @@ -5374,7 +5756,7 @@ C "Thank you" to MAPLE (probably spared one day of hand-differentiation). end #else C-------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) C C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral C angles gamma and its derivatives in consecutive thetas and gammas. @@ -5393,6 +5775,7 @@ C include 'COMMON.NAMES' include 'COMMON.FFIELD' include 'COMMON.CONTROL' + include 'COMMON.TORCNSTR' double precision coskt(mmaxtheterm),sinkt(mmaxtheterm), & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle), & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble), @@ -5403,8 +5786,7 @@ C c print *,i,itype(i-1),itype(i),itype(i-2) if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 & .or.itype(i).eq.ntyp1) cycle -C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF - +C print *,i,theta(i) if (iabs(itype(i+1)).eq.20) iblock=2 if (iabs(itype(i+1)).ne.20) iblock=1 dethetai=0.0d0 @@ -5416,6 +5798,7 @@ C In current verion the ALL DUMMY ATOM POTENTIALS ARE OFF coskt(k)=dcos(k*theti2) sinkt(k)=dsin(k*theti2) enddo +C print *,ethetai if (i.gt.3 .and. itype(i-3).ne.ntyp1) then #ifdef OSF phii=phi(i) @@ -5431,8 +5814,8 @@ C propagation of chirality for glycine type enddo else phii=0.0d0 - ityp1=nthetyp+1 do k=1,nsingle + ityp1=ithetyp((itype(i-2))) cosph1(k)=0.0d0 sinph1(k)=0.0d0 enddo @@ -5452,7 +5835,7 @@ C propagation of chirality for glycine type enddo else phii1=0.0d0 - ityp3=nthetyp+1 + ityp3=ithetyp((itype(i))) do k=1,nsingle cosph2(k)=0.0d0 sinph2(k)=0.0d0 @@ -5502,6 +5885,7 @@ C propagation of chirality for glycine type enddo write(iout,*) "ethetai",ethetai endif +C print *,ethetai do m=1,ntheterm2 do k=1,nsingle aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k) @@ -5522,10 +5906,16 @@ C propagation of chirality for glycine type & ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet", & ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet", & eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai +C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k) enddo enddo +C print *,"cosph1", (cosph1(k), k=1,nsingle) +C print *,"cosph2", (cosph2(k), k=1,nsingle) +C print *,"sinph1", (sinph1(k), k=1,nsingle) +C print *,"sinph2", (sinph2(k), k=1,nsingle) if (lprn) & write(iout,*) "ethetai",ethetai +C print *,"tu",cosph1(k),sinph1(k),cosph2(k),sinph2(k) do m=1,ntheterm3 do k=2,ndouble do l=1,k-1 @@ -5561,6 +5951,7 @@ C propagation of chirality for glycine type enddo 10 continue c lprn1=.true. +C print *,ethetai if (lprn1) & write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') & i,theta(i)*rad2deg,phii*rad2deg, @@ -5569,8 +5960,37 @@ c lprn1=.false. etheta=etheta+ethetai if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 - gloc(nphi+i-2,icg)=wang*dethetai+gloc(nphi+i-2,icg) + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*dethetai enddo +C now constrains + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=ithetaconstr_start,ithetaconstr_end + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", + & i,itheta,rad2deg*thetiii, + & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), + & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, + & gloc(itheta+nphi-2,icg) + endif + enddo + return end #endif @@ -6390,12 +6810,12 @@ c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) difi=phii-phi0(i) if (difi.gt.drange(i)) then difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 else if (difi.lt.-drange(i)) then difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)**difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 endif ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii, ! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) @@ -6501,18 +6921,21 @@ c do i=1,ndih_constr difi=pinorm(phii-phi0(i)) if (difi.gt.drange(i)) then difi=difi-drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 else if (difi.lt.-drange(i)) then difi=difi+drange(i) - edihcnstr=edihcnstr+0.25d0*ftors*difi**4 - gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3 + edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4 + gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3 else difi=0.0 endif -cd write (iout,'(2i5,4f8.3,2e14.5)') i,itori,rad2deg*phii, -cd & rad2deg*phi0(i), rad2deg*drange(i), -cd & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg) + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "edihc", + & i,itori,rad2deg*phii, + & rad2deg*phi0(i), rad2deg*drange(i), + & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg) + endif enddo cd write (iout,*) 'edihcnstr',edihcnstr return @@ -8589,9 +9012,9 @@ cd ghalf=0.0d0 cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k) cgrad ghalf=0.5d0*ggg2(ll) cd ghalf=0.0d0 - gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2) + gradcorr5(ll,k)=gradcorr5(ll,k)+ekont*derx(ll,2,2) gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2) - gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2) + gradcorr5(ll,l)=gradcorr5(ll,l)+ekont*derx(ll,4,2) gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2) gradcorr5_long(ll,l)=gradcorr5_long(ll,l)+gradcorr5kl gradcorr5_long(ll,k)=gradcorr5_long(ll,k)-gradcorr5kl @@ -9900,4 +10323,319 @@ crc print *,((prod(i,j),i=1,2),j=1,2) return end +CCC---------------------------------------------- + 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.NAMES' + 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=ilip_start,ilip_end +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 + +C print *,"doing sccale for lower part" +C print *,i,sslip,fracinbuf,ssgradlip + 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=ilip_start,ilip_end + 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 +C--------------------------------------------------------- +C AFM soubroutine for constant force + subroutine AFMforce(Eafmforce) + 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.NAMES' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' + real*8 diffafm(3) + dist=0.0d0 + Eafmforce=0.0d0 + do i=1,3 + diffafm(i)=c(i,afmend)-c(i,afmbeg) + dist=dist+diffafm(i)**2 + enddo + dist=dsqrt(dist) + Eafmforce=-forceAFMconst*(dist-distafminit) + do i=1,3 + gradafm(i,afmend-1)=-forceAFMconst*diffafm(i)/dist + gradafm(i,afmbeg-1)=forceAFMconst*diffafm(i)/dist + enddo +C print *,'AFM',Eafmforce + return + end +C--------------------------------------------------------- +C AFM subroutine with pseudoconstant velocity + subroutine AFMvel(Eafmforce) + 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.NAMES' + include 'COMMON.INTERACT' + include 'COMMON.IOUNITS' + include 'COMMON.CALC' + include 'COMMON.CONTROL' + include 'COMMON.SPLITELE' + include 'COMMON.SBRIDGE' + real*8 diffafm(3) +C Only for check grad COMMENT if not used for checkgrad +C totT=3.0d0 +C-------------------------------------------------------- +C print *,"wchodze" + dist=0.0d0 + Eafmforce=0.0d0 + do i=1,3 + diffafm(i)=c(i,afmend)-c(i,afmbeg) + dist=dist+diffafm(i)**2 + enddo + dist=dsqrt(dist) + Eafmforce=0.5d0*forceAFMconst + & *(distafminit+totTafm*velAFMconst-dist)**2 +C Eafmforce=-forceAFMconst*(dist-distafminit) + do i=1,3 + gradafm(i,afmend-1)=-forceAFMconst* + &(distafminit+totTafm*velAFMconst-dist) + &*diffafm(i)/dist + gradafm(i,afmbeg-1)=forceAFMconst* + &(distafminit+totTafm*velAFMconst-dist) + &*diffafm(i)/dist + enddo +C print *,'AFM',Eafmforce,totTafm*velAFMconst,dist + return + end +C----------------------------------------------------------- +C first for shielding is setting of function of side-chains + subroutine set_shield_fac + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +C this is the squar root 77 devided by 81 the epislion in lipid (in protein) + double precision div77_81/0.974996043d0/, + &div4_81/0.2222222222d0/ + +C the vector between center of side_chain and peptide group + double precision pep_side(3),long,side_calf(3), + &pept_group(3) +C the line belowe needs to be changed for FGPROC>1 + do i=1,nres-1 + if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle + ishield_list(i)=0 +Cif there two consequtive dummy atoms there is no peptide group between them +C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(k+nres,j)-(c(i,j)+c(i+1,j))/2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(k+nres,j)-c(k,j) + pept_group(j)=c(i,j)-c(i+1,j) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C now sscale + if (sh_frac_dist.le.0.0) cycle +C If we reach here it means that this side chain reaches the shielding sphere +C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i))=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0*sh_frac_dist-3.0d0) + fac_help_scale=6.0*(scale_fac_dist-scale_fac_dist**2) + & /dist_pep_side/buff_shield*0.5 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) + enddo + endif +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1+short**2/dist_pep_side**2) +C now costhet_grad + costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**3 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + fac_alfa_sin=1.0-(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf))**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short + cosphi=1.0d0/dsqrt(1+rkprim**2/dist_pep_side**2) + VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi) + & /VSolvSphere_div +C now the gradient... +C grad_shield is gradient of Calfa for peptide groups + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +sh_frac_dist_grad(j)*VofOverlap +C gradient po costhet + &+scale_fac_dist*costhet_grad(j) +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & sh_frac_dist_grad(j)*VofOverlap*2.0d0 + & +scale_fac_dist*costhet_grad(j)*2.0d0 +C grad_shield_side_ca is Calfa sidechain gradient + grad_shield_side_ca(j,ishield_list(i),i)= + enddo + VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist +C if ((cosphi.le.0.0).or.(costhet.le.0.0)) write(iout,*) "ERROR", +C & cosphi,costhet +C now should be fac_side_grad(k) which will be gradient of factor k which also +C affect the gradient of peptide group i fac_pept_grad(i) and i+1 + write(2,*) "myvolume",VofOverlap,VSolvSphere_div,VolumeTotal + enddo +C write(2,*) "TOTAL VOLUME",i,VolumeTotal +C the scaling factor of the shielding effect + fac_shield(i)=VolumeTotal*div77_81+div4_81 + write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i) + enddo + return + end