include 'COMMON.INTERACT'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
+ include 'COMMON.SHIELD'
+ include 'COMMON.CONTROL'
double precision fact(6)
cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot
cd print *,'nnt=',nnt,' nct=',nct
C
C Calculate electrostatic (H-bonding) energy of the main chain.
C
- 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
+ 106 continue
+ if (shield_mode.eq.1) then
+ call set_shield_fac
+ else if (shield_mode.eq.2) then
+ call set_shield_fac2
+ endif
+ call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
C write(iout,*) 'po eelec'
C Calculate excluded-volume interaction energy between peptide groups
C
C Calculate the virtual-bond-angle energy.
C
- call ebend(ebe)
C print *,'Bend energy finished.'
+ call ebend(ebe,ethetacnstr)
+cd print *,'Bend energy finished.'
C
C Calculate the SC local energy.
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
call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
c print *,ecorr,ecorr5,ecorr6,eturn6
+ else
+ ecorr=0.0d0
+ ecorr5=0.0d0
+ ecorr6=0.0d0
+ eturn6=0.0d0
endif
if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then
call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
endif
c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
#ifdef SPLITELE
+ if (shield_mode.gt.0) then
+ etot=fact(1)*wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2
+ & +welec*fact(1)*ees
+ & +fact(1)*wvdwpp*evdw1
+ & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
+ & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
+ & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
+ else
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
& +wvdwpp*evdw1
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
+ endif
#else
+ if (shield_mode.gt.0) then
+ etot=fact(1)wsc*(evdw+fact(6)*evdw_t)+fact(1)*wscp*evdw2
+ & +welec*fact(1)*(ees+evdw1)
+ & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
+ & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
+ & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
+ else
etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
& +welec*fact(1)*(ees+evdw1)
& +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
- & +wstrain*ehpb+nss*ebr+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
+ & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
& +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
& +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
& +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
- & +wbond*estr+wsccor*fact(1)*esccor
+ & +wbond*estr+wsccor*fact(1)*esccor+ethetacnstr
+ & +wliptran*eliptran
+ endif
#endif
energia(0)=etot
energia(1)=evdw
energia(19)=esccor
energia(20)=edihcnstr
energia(21)=evdw_t
+ energia(24)=ethetacnstr
+ energia(22)=eliptran
c detecting NaNQ
#ifdef ISNAN
#ifdef AIX
#ifdef MPL
c endif
#endif
+#define DEBUG
+#ifdef DEBUG
+ call enerprint(energia,fact)
+#endif
+#undef DEBUG
if (calc_grad) then
C
C Sum up the components of the Cartesian gradient.
#ifdef SPLITELE
do i=1,nct
do j=1,3
+ if (shield_mode.eq.0) then
gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
& welec*fact(1)*gelc(j,i)+wvdwpp*gvdwpp(j,i)+
& wbond*gradb(j,i)+
& 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)
+ else
+ gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)
+ & +fact(1)*wscp*gvdwc_scp(j,i)+
+ & welec*fact(1)*gelc(j,i)+fact(1)*wvdwpp*gvdwpp(j,i)+
+ & wbond*gradb(j,i)+
+ & wstrain*ghpbc(j,i)+
+ & wcorr*fact(3)*gradcorr(j,i)+
+ & wel_loc*fact(2)*gel_loc(j,i)+
+ & wturn3*fact(2)*gcorr3_turn(j,i)+
+ & wturn4*fact(3)*gcorr4_turn(j,i)+
+ & wcorr5*fact(4)*gradcorr5(j,i)+
+ & wcorr6*fact(5)*gradcorr6(j,i)+
+ & wturn6*fact(5)*gcorr6_turn(j,i)+
+ & wsccor*fact(2)*gsccorc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +welec*gshieldc(j,i)
+ & +welec*gshieldc_loc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wcorr*gshieldc_loc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn3*gshieldc_loc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wturn4*gshieldc_loc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+ & +wel_loc*gshieldc_loc_ll(j,i)
+
+ gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i)
+ & +fact(1)*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)
+ & +welec*gshieldx(j,i)
+ & +wcorr*gshieldx_ec(j,i)
+ & +wturn3*gshieldx_t3(j,i)
+ & +wturn4*gshieldx_t4(j,i)
+ & +wel_loc*gshieldx_ll(j,i)
+
+
+ endif
enddo
#else
do i=1,nct
do j=1,3
+ if (shield_mode.eq.0) then
gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
& welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+
& wbond*gradb(j,i)+
& 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)
+ else
+ gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)+
+ & fact(1)*wscp*gvdwc_scp(j,i)+
+ & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+
+ & wbond*gradb(j,i)+
+ & wcorr*fact(3)*gradcorr(j,i)+
+ & wel_loc*fact(2)*gel_loc(j,i)+
+ & wturn3*fact(2)*gcorr3_turn(j,i)+
+ & wturn4*fact(3)*gcorr4_turn(j,i)+
+ & wcorr5*fact(4)*gradcorr5(j,i)+
+ & wcorr6*fact(5)*gradcorr6(j,i)+
+ & wturn6*fact(5)*gcorr6_turn(j,i)+
+ & wsccor*fact(2)*gsccorc(j,i)
+ & +wliptran*gliptranc(j,i)
+ & +welec*gshieldc(j,i)
+ & +welec*gshieldc_loc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wcorr*gshieldc_loc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn3*gshieldc_loc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wturn4*gshieldc_loc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+ & +wel_loc*gshieldc_loc_ll(j,i)
+
+ gradx(j,i,icg)=fact(1)*wsc*gvdwx(j,i)+
+ & fact(1)*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)
+ & +welec*gshieldx(j,i)
+ & +wcorr*gshieldx_ec(j,i)
+ & +wturn3*gshieldx_t3(j,i)
+ & +wturn4*gshieldx_t4(j,i)
+ & +wel_loc*gshieldx_ll(j,i)
+
+ endif
enddo
#endif
enddo
& +wturn3*fact(2)*gel_loc_turn3(i)
& +wturn6*fact(5)*gel_loc_turn6(i)
& +wel_loc*fact(2)*gel_loc_loc(i)
+c & +wsccor*fact(1)*gsccor_loc(i)
+c BYLA ROZNICA Z CLUSTER< OSTATNIA LINIA DODANA
enddo
endif
+ if (dyn_ss) call dyn_set_nss
return
end
C------------------------------------------------------------------------
esccor=energia(19)
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,
& 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,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)'/
& '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)'/
+ & '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,
& 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,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)'/
& '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)'/
+ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/
& 'ETOT= ',1pE16.6,' (total)')
#endif
return
integer icant
external icant
cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+c ROZNICA z cluster
do i=1,210
do j=1,2
eneps_temp(j,i)=0.0d0
enddo
enddo
+cROZNICA
+
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
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
eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
+c
+
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 & 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
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)
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
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
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,
include 'COMMON.ENEPS'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
- integer icant
+ integer icant,xshift,yshift,zshift
external icant
do i=1,210
do j=1,2
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)
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
+ call dyn_ssbond_ene(i,j,evdwij)
+ evdw=evdw+evdwij
+C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+C & 'evdw',i,j,evdwij,' ss',evdw,evdw_t
+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
+ call triple_ssbond_ene(i,j,k,evdwij)
+C call the energy function that removes the artifical triple disulfide
+C bond the soubroutine is located in ssMD.F
+ evdw=evdw+evdwij
+C write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+C & 'evdw',i,j,evdwij,'tss',evdw,evdw_t
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
ind=ind+1
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
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)) then
+
+C write(iout,*) "tu,", i,j,aa_aq(itypi,itypj)-aa,
+C & bb_aq(itypi,itypj)-bb,
+C & sslipi,sslipj
+C endif
+
+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
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)
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
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
+C#define DEBUG
#ifdef DEBUG
write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& evdwij
write (iout,*) "partial sum", evdw, evdw_t
#endif
+C#undef DEBUG
c endif
if (calc_grad) then
C Calculate gradient components.
C Calculate angular part of the gradient.
call sc_grad
endif
+C write(iout,*) "partial sum", evdw, evdw_t
+ ENDIF ! dyn_ss
enddo ! j
enddo ! iint
enddo ! i
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
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))
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
+ 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),
gcorr_loc(i)=0.0d0
enddo
do i=iatel_s,iatel_e
- if (i.eq.1) then
+C if (i.eq.1) then
if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1
- & .or. itype(i+2).eq.ntyp1) cycle
- else
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
- & .or. itype(i+2).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
+C & .or. itype(i+2).eq.ntyp1) cycle
+C else
+C if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C & .or. itype(i+2).eq.ntyp1
+C & .or. itype(i-1).eq.ntyp1
&) cycle
- endif
+C endif
if (itel(i).eq.0) goto 1215
dxi=dc(1,i)
dyi=dc(2,i)
num_conti=0
C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (j.eq.1) then
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
- & .or.itype(j+2).eq.ntyp1
- &) cycle
- else
+ if (j.le.1) cycle
+C if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
+C & .or.itype(j+2).eq.ntyp1
+C &) cycle
+C else
if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
- & .or.itype(j+2).eq.ntyp1
- & .or.itype(j-1).eq.ntyp1
+C & .or.itype(j+2).eq.ntyp1
+C & .or.itype(j-1).eq.ntyp1
&) cycle
- endif
+C endif
C
C) cycle
if (itel(j).eq.0) goto 1216
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
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
xj_safe=xj
yj_safe=yj
zj_safe=zj
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
+ 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=yj_safe-ymedi
zj=zj_safe-zmedi
endif
-
rij=xj*xj+yj*yj+zj*zj
sss=sscale(sqrt(rij))
sssgrad=sscagrad(sqrt(rij))
c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij
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
+C#define DEBUG
+#ifdef DEBUG
+ write(iout,*) "ees_compon",i,j,el1,el2,
+ & fac_shield(i),fac_shield(j)
+#endif
+C#undef DEBUG
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ el1=el1*fac_shield(i)**2*fac_shield(j)**2
+ el2=el2*fac_shield(i)**2*fac_shield(j)**2
+ eesij=(el1+el2)
ees=ees+eesij
+ else
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+ eesij=(el1+el2)
+ ees=ees+eesij
+ endif
evdw1=evdw1+evdwij*sss
c write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
c &'evdw1',i,j,evdwij
ggg(1)=facel*xj
ggg(2)=facel*yj
ggg(3)=facel*zj
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eesij/fac_shield(i)
+ & *2.0
+ gshieldx(k,iresshield)=gshieldx(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)*2.0
+ gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield
+C gshieldc_loc(k,iresshield)=gshieldc_loc(k,iresshield)
+C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)
+C if (iresshield.gt.i) then
+C do ishi=i+1,iresshield-1
+C gshieldc(k,ishi)=gshieldc(k,ishi)+rlocshield
+C & +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)
+C
+C enddo
+C else
+C do ishi=iresshield,i
+C gshieldc(k,ishi)=gshieldc(k,ishi)-rlocshield
+C & -grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)
+C
+C enddo
+C endif
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eesij/fac_shield(j)
+ & *2.0
+ gshieldx(k,iresshield)=gshieldx(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0
+ gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc(k,i)=gshieldc(k,i)+
+ & grad_shield(k,i)*eesij/fac_shield(i)*2.0
+ gshieldc(k,j)=gshieldc(k,j)+
+ & grad_shield(k,j)*eesij/fac_shield(j)*2.0
+ gshieldc(k,i-1)=gshieldc(k,i-1)+
+ & grad_shield(k,i)*eesij/fac_shield(i)*2.0
+ gshieldc(k,j-1)=gshieldc(k,j-1)+
+ & grad_shield(k,j)*eesij/fac_shield(j)*2.0
+
+ enddo
+ endif
+
do k=1,3
ghalf=0.5D0*ggg(k)
gelc(k,i)=gelc(k,i)+ghalf
cd & (dcosg(k),k=1,3)
do k=1,3
ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+ & *fac_shield(i)**2*fac_shield(j)**2
enddo
do k=1,3
ghalf=0.5D0*ggg(k)
gelc(k,i)=gelc(k,i)+ghalf
& +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
& + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ & *fac_shield(i)**2*fac_shield(j)**2
+
gelc(k,j)=gelc(k,j)+ghalf
& +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
& + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ & *fac_shield(i)**2*fac_shield(j)**2
enddo
do k=i+1,j-1
do l=1,3
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)
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
+ eel_loc_ij=eel_loc_ij
+ & *fac_shield(i)*fac_shield(j)
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)
+C eel_loc=eel_loc+eel_loc_ij
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij
+ & /fac_shield(i)
+C & *2.0
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eel_loc_ij
+ & /fac_shield(j)
+C & *2.0
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j)
+ gshieldc_ll(k,iresshield-1)=gshieldc_ll(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+ do k=1,3
+ gshieldc_ll(k,i)=gshieldc_ll(k,i)+
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,j)=gshieldc_ll(k,j)+
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+
+ & grad_shield(k,i)*eel_loc_ij/fac_shield(i)
+ gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+
+ & grad_shield(k,j)*eel_loc_ij/fac_shield(j)
+ enddo
+ endif
eel_loc=eel_loc+eel_loc_ij
+
C Partial derivatives in virtual-bond dihedral angles gamma
if (calc_grad) then
if (i.gt.1)
& gel_loc_loc(i-1)=gel_loc_loc(i-1)+
- & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
- & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)
+ & (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
+ & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j))
+ & *fac_shield(i)*fac_shield(j)
+
gel_loc_loc(j-1)=gel_loc_loc(j-1)+
- & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
- & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)
+ & (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
+ & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j))
+ & *fac_shield(i)*fac_shield(j)
+
cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij)
cd write(iout,*) 'agg ',agg
cd write(iout,*) 'aggi ',aggi
C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
do l=1,3
- ggg(l)=agg(l,1)*muij(1)+
- & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)
+ ggg(l)=(agg(l,1)*muij(1)+
+ & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
enddo
do k=i+2,j2
do l=1,3
enddo
C Remaining derivatives of eello
do l=1,3
- gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
- & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
- gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
- & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
- gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
- & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
- gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
- & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
+ gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+
+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+
+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+
+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
+ gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+
+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4))
+ & *fac_shield(i)*fac_shield(j)
+
enddo
endif
ENDIF
ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
c ees0mij=0.0D0
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0d0
+ fac_shield(j)=1.0d0
+ else
+ ees0plist(num_conti,i)=j
+C fac_shield(i)=0.4d0
+C fac_shield(j)=0.6d0
+ endif
ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
+ & *fac_shield(i)*fac_shield(j)
+
ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
+ & *fac_shield(i)*fac_shield(j)
+
C Diagnostics. Comment out or remove after debugging!
c ees0p(num_conti,i)=0.5D0*fac3*ees0pij
c ees0m(num_conti,i)=0.5D0*fac3*ees0mij
gacontp_hb1(k,num_conti,i)=ghalfp
& +(ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i))
& + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ & *fac_shield(i)*fac_shield(j)
+
gacontp_hb2(k,num_conti,i)=ghalfp
& +(ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j))
& + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ & *fac_shield(i)*fac_shield(j)
+
gacontp_hb3(k,num_conti,i)=gggp(k)
+ & *fac_shield(i)*fac_shield(j)
+
gacontm_hb1(k,num_conti,i)=ghalfm
& +(ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i))
& + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ & *fac_shield(i)*fac_shield(j)
+
gacontm_hb2(k,num_conti,i)=ghalfm
& +(ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j))
& + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ & *fac_shield(i)*fac_shield(j)
+
gacontm_hb3(k,num_conti,i)=gggm(k)
+ & *fac_shield(i)*fac_shield(j)
+
enddo
endif
C Diagnostics. Comment out or remove after debugging!
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
+ include 'COMMON.SHIELD'
+ include 'COMMON.CONTROL'
dimension ggg(3)
double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
& e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
& aggj(3,4),aggj1(3,4),a_temp(2,2)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
if (j.eq.i+2) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+C & .or.((i+5).gt.nres)
+C & .or.((i-1).le.0)
+C end of changes suggested by Ana
+ & .or. itype(i+2).eq.ntyp1
+ & .or. itype(i+3).eq.ntyp1
+C & .or. itype(i+5).eq.ntyp1
+C & .or. itype(i).eq.ntyp1
+C & .or. itype(i-1).eq.ntyp1
+ & ) goto 179
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Third-order contributions
call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
call transpose2(auxmat(1,1),auxmat1(1,1))
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
+
eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+ eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
cd write (2,*) 'i,',i,' j',j,'eello_turn3',
cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
cd & ' eello_turn3_num',4*eello_turn3_num
if (calc_grad) then
+C Derivatives in shield mode
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t3/fac_shield(i)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t3/fac_shield(j)
+C & *2.0
+ gshieldx_t3(k,iresshield)=gshieldx_t3(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,iresshield-1)=gshieldc_t3(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t3(k,i)=gshieldc_t3(k,i)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j)=gshieldc_t3(k,j)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ gshieldc_t3(k,i-1)=gshieldc_t3(k,i-1)+
+ & grad_shield(k,i)*eello_t3/fac_shield(i)
+ gshieldc_t3(k,j-1)=gshieldc_t3(k,j-1)+
+ & grad_shield(k,j)*eello_t3/fac_shield(j)
+ enddo
+ endif
+
C Derivatives in gamma(i)
call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1))
call transpose2(auxmat2(1,1),pizda(1,1))
call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
C Derivatives in gamma(i+1)
call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
call transpose2(auxmat2(1,1),pizda(1,1))
call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
C Cartesian derivatives
do l=1,3
a_temp(1,1)=aggi(l,1)
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,i)=gcorr3_turn(l,i)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
a_temp(2,1)=aggi1(l,3)
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
a_temp(2,1)=aggj(l,3)
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,j)=gcorr3_turn(l,j)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
+ & *fac_shield(i)*fac_shield(j)
+
enddo
endif
+ 179 continue
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
+C & .or.((i+5).gt.nres)
+C & .or.((i-1).le.0)
+C end of changes suggested by Ana
+ & .or. itype(i+3).eq.ntyp1
+ & .or. itype(i+4).eq.ntyp1
+C & .or. itype(i+5).eq.ntyp1
+ & .or. itype(i).eq.ntyp1
+C & .or. itype(i-1).eq.ntyp1
+ & ) goto 178
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.4
+C fac_shield(j)=0.6
+ endif
+
eello_turn4=eello_turn4-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+ eello_t4=-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
cd & ' eello_turn4_num',8*eello_turn4_num
C Derivatives in gamma(i)
if (calc_grad) then
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (shield_mode.gt.0)) then
+C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eello_t4/fac_shield(i)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,j)*eello_t4/fac_shield(j)
+C & *2.0
+ gshieldx_t4(k,iresshield)=gshieldx_t4(k,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(k,ilist,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,iresshield-1)=gshieldc_t4(k,iresshield-1)
+ & +rlocshield
+
+ enddo
+ enddo
+
+ do k=1,3
+ gshieldc_t4(k,i)=gshieldc_t4(k,i)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j)=gshieldc_t4(k,j)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ gshieldc_t4(k,i-1)=gshieldc_t4(k,i-1)+
+ & grad_shield(k,i)*eello_t4/fac_shield(i)
+ gshieldc_t4(k,j-1)=gshieldc_t4(k,j-1)+
+ & grad_shield(k,j)*eello_t4/fac_shield(j)
+ enddo
+ endif
call transpose2(EUgder(1,1,i+1),e1tder(1,1))
call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1))
call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
+ & *fac_shield(i)*fac_shield(j)
+
C Derivatives in gamma(i+1)
call transpose2(EUgder(1,1,i+2),e2tder(1,1))
call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
C Derivatives in gamma(i+2)
call transpose2(EUgder(1,1,i+3),e3tder(1,1))
call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
C Cartesian derivatives
+
C Derivatives of this turn contributions in DC(i+2)
if (j.lt.nres-1) then
do l=1,3
s3=0.5d0*(pizda(1,1)+pizda(2,2))
ggg(l)=-(s1+s2+s3)
gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
enddo
endif
C Remaining derivatives of this turn contribution
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
a_temp(2,1)=aggi1(l,3)
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
a_temp(2,1)=aggj(l,3)
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
+
enddo
endif
+ 178 continue
endif
return
end
include 'COMMON.DERIV'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
dimension ggg(3)
ehpb=0.0D0
cd print *,'edis: nhpb=',nhpb,' fbr=',fbr
cd print *,'link_start=',link_start,' link_end=',link_end
+C write(iout,*) link_end, "link_end"
if (link_end.eq.0) return
do i=link_start,link_end
C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
endif
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.
+C if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
+C & iabs(itype(jjj)).eq.1) then
+C write(iout,*) constr_dist,"const"
+ if (.not.dyn_ss .and. i.le.nss) 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
- else
-C Calculate the distance between the two points and its difference from the
-C target distance.
- dd=dist(ii,jj)
- rdis=dd-dhpb(i)
+ endif !ii.gt.neres
+ 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
+C ehpb=ehpb+fordepth(i)**4.0d0
+C & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+ 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
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & ehpb,fordepth(i),dd
+C write(iout,*) ehpb,"atu?"
+C ehpb,"tu?"
+C fac=fordepth(i)**4.0d0
+C & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(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 !end dhpb1(i).gt.0
+ endif !end const_dist=11
+ 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 !ii.gt.nres
+C write(iout,*) "before"
+ dd=dist(ii,jj)
+C write(iout,*) "after",dd
+ 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
+C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
+C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
+C print *,ehpb,"tu?"
+C write(iout,*) ehpb,"btu?",
+C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i)
+C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
+C & 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)
+ waga=forcon(i)
C Calculate the contribution to energy.
- ehpb=ehpb+waga*rdis*rdis
+ 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
+ fac=waga*rdis/dd
+ endif
+ endif
+
do j=1,3
ggg(j)=fac*(c(j,jj)-c(j,ii))
enddo
enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
C--------------------------------------------------------------------------
C else
if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
diff = vbld(i)-vbldpDUM
+C write(iout,*) i,diff
else
diff = vbld(i)-vbldp0
c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
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.
include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
+ 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
double precision y(2),z(2)
delta=0.02d0*pi
- time11=dexp(-2*time)
- time12=1.0d0
+c time11=dexp(-2*time)
+c time12=1.0d0
etheta=0.0D0
c write (iout,*) "nres",nres
c write (*,'(a,i2)') 'EBEND ICG=',icg
if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
- icrc=0
- call proc_proc(phii,icrc)
+c icrc=0
+c call proc_proc(phii,icrc)
if (icrc.eq.1) phii=150.0
#else
phii=phi(i)
if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
- icrc=0
- call proc_proc(phii1,icrc)
+c icrc=0
+c call proc_proc(phii1,icrc)
if (icrc.eq.1) phii1=150.0
phii1=pinorm(phii1)
z(1)=cos(phii1)
if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
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)
- 1215 continue
+c 1215 continue
+ enddo
+ ethetacnstr=0.0d0
+C print *,ithetaconstr_start,ithetaconstr_end,"TU"
+ do i=1,ntheta_constr
+ 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
+C if (energy_dec) then
+C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+C & i,itheta,rad2deg*thetiii,
+C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+C & gloc(itheta+nphi-2,icg)
+C endif
enddo
C Ufff.... We've done all this!!!
return
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.
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),
enddo
else
phii=0.0d0
- ityp1=nthetyp+1
+c ityp1=nthetyp+1
do k=1,nsingle
+ ityp1=ithetyp((itype(i-2)))
cosph1(k)=0.0d0
sinph1(k)=0.0d0
enddo
enddo
else
phii1=0.0d0
- ityp3=nthetyp+1
+c ityp3=nthetyp+1
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
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
+c gloc(nphi+i-2,icg)=wang*dethetai
+ 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=1,ntheta_constr
+ 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
+C if (energy_dec) then
+C write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc",
+C & i,itheta,rad2deg*thetiii,
+C & rad2deg*theta_constr0(i), rad2deg*theta_drange(i),
+C & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4,
+C & gloc(itheta+nphi-2,icg)
+C endif
enddo
return
end
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)
+C write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih",
+C & i,itori,rad2deg*phii,
+C & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg)
enddo
! write (iout,*) 'edihcnstr',edihcnstr
return
edihi=0.0d0
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
- edihi=0.25d0*ftors*difi**4
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ edihi=0.25d0*ftors(i)*difi**4
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
- edihi=0.25d0*ftors*difi**4
+ edihcnstr=edihcnstr+0.25d0*ftors(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ edihi=0.25d0*ftors(i)*difi**4
else
difi=0.0d0
endif
+ write (iout,'(a6,2i5,2f8.3,2e14.5)') "edih",
+ & i,itori,rad2deg*phii,
+ & rad2deg*difi,0.25d0*ftors(i)*difi**4
c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi,
c & drange(i),edihi
! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
+! & rad2deg*difi,0.25d0*ftors(i)*difi**4,gloc(itori-3,icg)
enddo
! write (iout,*) 'edihcnstr',edihcnstr
return
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+C write (iout,*)"EBACK_SC_COR",esccor,i
c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp,
c & nterm_sccor(isccori,isccori1),isccori,isccori1
c gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
C Set lprn=.true. for debugging
lprn=.false.
eturn6=0.0d0
+ ecorr6=0.0d0
#ifdef MPL
n_corr=0
n_corr1=0
cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
eturn6=eturn6+eello_turn6(i,jj,kk)
cd write (2,*) 'multibody_eello:eturn6',eturn6
+ else if ((wturn6.eq.0.0d0).and.(wcorr6.eq.0.0d0)) then
+ eturn6=0.0d0
+ ecorr6=0.0d0
endif
+
ENDIF
1111 continue
else if (j1.eq.j) then
enddo ! kk
enddo ! jj
enddo ! i
+ write (iout,*) "eturn6",eturn6,ecorr6
return
end
c------------------------------------------------------------------------------
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
logical lprn
lprn=.false.
c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
C Calculate the multi-body contribution to energy.
- ecorr=ecorr+ekont*ees
+C ecorr=ecorr+ekont*ees
if (calc_grad) then
C Calculate multi-body contributions to the gradient.
do ll=1,3
& ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
& coeffm*ees0mij*gacontm_hb3(ll,kk,k))
enddo
- enddo
+ enddo
+ if (shield_mode.gt.0) then
+ j=ees0plist(jj,i)
+ l=ees0plist(kk,k)
+C print *,i,j,fac_shield(i),fac_shield(j),
+C &fac_shield(k),fac_shield(l)
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and.
+ & (fac_shield(k).gt.0).and.(fac_shield(l).gt.0)) then
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do m=1,3
+ rlocshield=grad_shield_side(m,ilist,i)*ehbcorr/fac_shield(i)
+C & *2.0
+ gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(m,ilist,i)*ehbcorr/fac_shield(i)
+ gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1)
+ &+rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(j)
+ iresshield=shield_list(ilist,j)
+ do m=1,3
+ rlocshield=grad_shield_side(m,ilist,j)*ehbcorr/fac_shield(j)
+C & *2.0
+ gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(m,ilist,j)*ehbcorr/fac_shield(j)
+ gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(k)
+ iresshield=shield_list(ilist,k)
+ do m=1,3
+ rlocshield=grad_shield_side(m,ilist,k)*ehbcorr/fac_shield(k)
+C & *2.0
+ gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(m,ilist,k)*ehbcorr/fac_shield(k)
+ gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+ do ilist=1,ishield_list(l)
+ iresshield=shield_list(ilist,l)
+ do m=1,3
+ rlocshield=grad_shield_side(m,ilist,l)*ehbcorr/fac_shield(l)
+C & *2.0
+ gshieldx_ec(m,iresshield)=gshieldx_ec(m,iresshield)+
+ & rlocshield
+ & +grad_shield_loc(m,ilist,l)*ehbcorr/fac_shield(l)
+ gshieldc_ec(m,iresshield-1)=gshieldc_ec(m,iresshield-1)
+ & +rlocshield
+ enddo
+ enddo
+C print *,gshieldx(m,iresshield)
+ do m=1,3
+ gshieldc_ec(m,i)=gshieldc_ec(m,i)+
+ & grad_shield(m,i)*ehbcorr/fac_shield(i)
+ gshieldc_ec(m,j)=gshieldc_ec(m,j)+
+ & grad_shield(m,j)*ehbcorr/fac_shield(j)
+ gshieldc_ec(m,i-1)=gshieldc_ec(m,i-1)+
+ & grad_shield(m,i)*ehbcorr/fac_shield(i)
+ gshieldc_ec(m,j-1)=gshieldc_ec(m,j-1)+
+ & grad_shield(m,j)*ehbcorr/fac_shield(j)
+
+ gshieldc_ec(m,k)=gshieldc_ec(m,k)+
+ & grad_shield(m,k)*ehbcorr/fac_shield(k)
+ gshieldc_ec(m,l)=gshieldc_ec(m,l)+
+ & grad_shield(m,l)*ehbcorr/fac_shield(l)
+ gshieldc_ec(m,k-1)=gshieldc_ec(m,k-1)+
+ & grad_shield(m,k)*ehbcorr/fac_shield(k)
+ gshieldc_ec(m,l-1)=gshieldc_ec(m,l-1)+
+ & grad_shield(m,l)*ehbcorr/fac_shield(l)
+
+ enddo
+ endif
+ endif
endif
ehbcorr=ekont*ees
return
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'
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-----------------------------------------------------------------------
+ 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/,sh_frac_dist_grad(3)
+
+C the vector between center of side_chain and peptide group
+ double precision pep_side(3),long,side_calf(3),
+ &pept_group(3),costhet_grad(3),cosphi_grad_long(3),
+ &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(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
+ if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle
+ 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(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0
+C pep_side(j)=2.0d0
+C and vector conecting the side-chain with its proper calfa
+ side_calf(j)=c(j,k+nres)-c(j,k)
+C side_calf(j)=2.0d0
+ pept_group(j)=c(j,i)-c(j,i+1)
+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)
+ dist_side_calf=dsqrt(dist_side_calf)
+ do j=1,3
+ pep_side_norm(j)=pep_side(j)/dist_pep_side
+ side_calf_norm(j)=dist_side_calf
+ enddo
+C now sscale fraction
+ sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
+C print *,buff_shield,"buff"
+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),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*(sh_frac_dist-sh_frac_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)
+C print *,"jestem",scale_fac_dist,fac_help_scale,
+C & sh_frac_dist_grad(j)
+ enddo
+ endif
+C if ((i.eq.3).and.(k.eq.2)) then
+C print *,i,sh_frac_dist,dist_pep,fac_help_scale,scale_fac_dist
+C & ,"TU"
+C 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(1.0+short**2/dist_pep_side**2)
+C now costhet_grad
+C costhet=0.0d0
+ costhet_fac=costhet**3*short**2*(-0.5)/dist_pep_side**4
+C costhet_fac=0.0d0
+ 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
+ cosalfa=(pep_side0pept_group/
+ & (dist_pep_side*dist_side_calf))
+ fac_alfa_sin=1.0-cosalfa**2
+ fac_alfa_sin=dsqrt(fac_alfa_sin)
+ rkprim=fac_alfa_sin*(long-short)+short
+C now costhet_grad
+ cosphi=1.0d0/dsqrt(1.0+rkprim**2/dist_pep_side**2)
+ cosphi_fac=cosphi**3*rkprim**2*(-0.5)/dist_pep_side**4
+
+ do j=1,3
+ cosphi_grad_long(j)=cosphi_fac*pep_side(j)
+ &+cosphi**3*0.5/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa/
+ &((dist_pep_side*dist_side_calf))*
+ &((side_calf(j))-cosalfa*
+ &((pep_side(j)/dist_pep_side)*dist_side_calf))
+
+ cosphi_grad_loc(j)=cosphi**3*0.5/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa
+ &/((dist_pep_side*dist_side_calf))*
+ &(pep_side(j)-
+ &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side)
+ enddo
+
+ VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi)
+ & /VSolvSphere_div
+ & *wshield
+C now the gradient...
+C grad_shield is gradient of Calfa for peptide groups
+C write(iout,*) "shield_compon",i,k,VSolvSphere,scale_fac_dist,
+C & costhet,cosphi
+C write(iout,*) "cosphi_compon",i,k,pep_side0pept_group,
+C & dist_pep_side,dist_side_calf,c(1,k+nres),c(1,k),itype(k)
+ do j=1,3
+ grad_shield(j,i)=grad_shield(j,i)
+C gradient po skalowaniu
+ & +(sh_frac_dist_grad(j)
+C gradient po costhet
+ &-scale_fac_dist*costhet_grad(j)/(1.0-costhet)
+ &-scale_fac_dist*(cosphi_grad_long(j))
+ &/(1.0-cosphi) )*div77_81
+ &*VofOverlap
+C grad_shield_side is Cbeta sidechain gradient
+ grad_shield_side(j,ishield_list(i),i)=
+ & (sh_frac_dist_grad(j)*-2.0d0
+ & +scale_fac_dist*costhet_grad(j)*2.0d0/(1.0-costhet)
+ & +scale_fac_dist*(cosphi_grad_long(j))
+ & *2.0d0/(1.0-cosphi))
+ & *div77_81*VofOverlap
+
+ grad_shield_loc(j,ishield_list(i),i)=
+ & scale_fac_dist*cosphi_grad_loc(j)
+ & *2.0d0/(1.0-cosphi)
+ & *div77_81*VofOverlap
+ enddo
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+ enddo
+ fac_shield(i)=VolumeTotal*div77_81+div4_81
+C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+ enddo
+ return
+ end
+C--------------------------------------------------------------------------
+C first for shielding is setting of function of side-chains
+ subroutine set_shield_fac2
+ 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/,sh_frac_dist_grad(3)
+
+C the vector between center of side_chain and peptide group
+ double precision pep_side(3),long,side_calf(3),
+ &pept_group(3),costhet_grad(3),cosphi_grad_long(3),
+ &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(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
+ if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle
+ 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(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0
+C pep_side(j)=2.0d0
+C and vector conecting the side-chain with its proper calfa
+ side_calf(j)=c(j,k+nres)-c(j,k)
+C side_calf(j)=2.0d0
+ pept_group(j)=c(j,i)-c(j,i+1)
+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)
+ dist_side_calf=dsqrt(dist_side_calf)
+ do j=1,3
+ pep_side_norm(j)=pep_side(j)/dist_pep_side
+ side_calf_norm(j)=dist_side_calf
+ enddo
+C now sscale fraction
+ sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield
+C print *,buff_shield,"buff"
+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),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
+ & *(2.0d0*sh_frac_dist-3.0d0)
+ fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2)
+ & /dist_pep_side/buff_shield*0.5d0
+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)
+C sh_frac_dist_grad(j)=0.0d0
+C scale_fac_dist=1.0d0
+C print *,"jestem",scale_fac_dist,fac_help_scale,
+C & sh_frac_dist_grad(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(1.0d0+short**2/dist_pep_side**2)
+ sinthet=short/dist_pep_side*costhet
+C now costhet_grad
+C costhet=0.6d0
+C sinthet=0.8
+ costhet_fac=costhet**3*short**2*(-0.5d0)/dist_pep_side**4
+C sinthet_fac=costhet**2*0.5d0*(short**3/dist_pep_side**4*costhet
+C & -short/dist_pep_side**2/costhet)
+C costhet_fac=0.0d0
+ 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=0.0d0
+ do j=1,3
+ pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j)
+ enddo
+ cosalfa=(pep_side0pept_group/
+ & (dist_pep_side*dist_side_calf))
+ fac_alfa_sin=1.0d0-cosalfa**2
+ fac_alfa_sin=dsqrt(fac_alfa_sin)
+ rkprim=fac_alfa_sin*(long-short)+short
+C rkprim=short
+
+C now costhet_grad
+ cosphi=1.0d0/dsqrt(1.0d0+rkprim**2/dist_pep_side**2)
+C cosphi=0.6
+ cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4
+ sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/
+ & dist_pep_side**2)
+C sinphi=0.8
+ do j=1,3
+ cosphi_grad_long(j)=cosphi_fac*pep_side(j)
+ &+cosphi**3*0.5d0/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa/
+ &((dist_pep_side*dist_side_calf))*
+ &((side_calf(j))-cosalfa*
+ &((pep_side(j)/dist_pep_side)*dist_side_calf))
+C cosphi_grad_long(j)=0.0d0
+ cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim)
+ &*(long-short)/fac_alfa_sin*cosalfa
+ &/((dist_pep_side*dist_side_calf))*
+ &(pep_side(j)-
+ &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side)
+C cosphi_grad_loc(j)=0.0d0
+ enddo
+C print *,sinphi,sinthet
+ VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet))
+ & /VSolvSphere_div
+C & *wshield
+C now the gradient...
+ 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*VSolvSphere/VSolvSphere_div/4.0d0*
+ &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinphi/sinthet*costhet*costhet_grad(j)
+ & +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
+ & )*wshield
+C grad_shield_side is Cbeta sidechain gradient
+ grad_shield_side(j,ishield_list(i),i)=
+ & (sh_frac_dist_grad(j)*-2.0d0
+ & *VofOverlap
+ & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*
+ &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinphi/sinthet*costhet*costhet_grad(j)
+ & +sinthet/sinphi*cosphi*cosphi_grad_long(j)))
+ & )*wshield
+
+ grad_shield_loc(j,ishield_list(i),i)=
+ & scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0*
+ &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*(
+ & sinthet/sinphi*cosphi*cosphi_grad_loc(j)
+ & ))
+ & *wshield
+ enddo
+ VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
+ enddo
+ fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
+C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+C write(2,*) "TU",rpp(1,1),short,long,buff_shield
+ enddo
+ return
+ end
projects / unres.git / blobdiff