#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
+C 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
C Calculate the virtual-bond-angle energy.
C
if (wang.gt.0d0) then
- call ebend(ebe)
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
+ call ebend(ebe,ethetacnstr)
+ endif
+C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call ebend_kcc(ebe,ethetacnstr)
+ endif
else
ebe=0
+ ethetacnstr=0
endif
c print *,"Processor",myrank," computed UB"
C
C
cd print *,'nterm=',nterm
if (wtor.gt.0) then
+ if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then
call etor(etors,edihcnstr)
+ endif
+C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then
+ call etor(etors,edihcnstr)
+ endif
else
etors=0
edihcnstr=0
C
C 6/23/01 Calculate double-torsional energy
C
- if (wtor_d.gt.0) then
+ if ((wtor_d.gt.0).and.((tor_mode.eq.0).or.(tor_mode.eq.2))) then
call etor_d(etors_d)
else
etors_d=0
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
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"
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+wliptran*eliptran
+ & +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+Eafmforce
+ & +ethetacnstr
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1)
& +wang*ebe+wtor*etors+wscloc*escloc
& +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3
& +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d
& +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
+ & +Eafmforce
+ & +ethetacnstr
#endif
energia(0)=etot
c detecting NaNQ
& wturn6*gcorr6_turn_long(j,i)+
& wstrain*ghpbc(j,i)
& +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
+ & +welec*gshieldc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+
enddo
enddo
& wturn6*gcorr6_turn_long(j,i)+
& wstrain*ghpbc(j,i)
& +wliptran*gliptranc(j,i)
+ & +gradafm(j,i)
+ & +welec*gshieldc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+
+
enddo
enddo
#endif
do i=-1,nct
do j=1,3
#ifdef SPLITELE
+C print *,gradbufc(1,13)
+C print *,welec*gelc(1,13)
+C print *,wel_loc*gel_loc(1,13)
+C print *,0.5d0*(wscp*gvdwc_scpp(1,13))
+C print *,welec*gelc_long(1,13)+wvdwpp*gvdwpp(1,13)
+C print *,wel_loc*gel_loc_long(1,13)
+C print *,gradafm(1,13),"AFM"
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+
& wel_loc*gel_loc(j,i)+
& 0.5d0*(wscp*gvdwc_scpp(j,i)+
& wsccor*gsccorc(j,i)
& +wscloc*gscloc(j,i)
& +wliptran*gliptranc(j,i)
+ & +gradafm(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)
+
+
+
+
+
+
#else
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+
& wel_loc*gel_loc(j,i)+
& 0.5d0*(wscp*gvdwc_scpp(j,i)+
- & welec*gelc_long(j,i)
+ & welec*gelc_long(j,i)+
& wel_loc*gel_loc_long(j,i)+
& wcorr*gcorr_long(j,i)+
& wcorr5*gradcorr5_long(j,i)+
& wsccor*gsccorc(j,i)
& +wscloc*gscloc(j,i)
& +wliptran*gliptranc(j,i)
+ & +gradafm(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)
+
+
+
+
+
#endif
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wsccor*gsccorx(j,i)
& +wscloc*gsclocx(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)
+
+
+
enddo
enddo
#ifdef DEBUG
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,eliptran,wliptran,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)'/
& '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,
& 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,eliptran,wliptran,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)'/
& '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
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
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))
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
+ elseif (zj.gt.bufliptop) then
fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
if (zi.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
- & ((positi-bordlipbot)/lipbufthick)
+ & ((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-positi)/lipbufthick)
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
sslipi=sscalelip(fracinbuf)
ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
else
if (zj.lt.buflipbot) then
C what fraction I am in
fracinbuf=1.0d0-
- & ((positi-bordlipbot)/lipbufthick)
+ & ((zj-bordlipbot)/lipbufthick)
C lipbufthick is thickenes of lipid buffore
sslipj=sscalelip(fracinbuf)
ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
- fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
sslipj=sscalelip(fracinbuf)
ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
else
c write(iout,*) 'b1=',b1(1,i-2)
c write (iout,*) 'theta=', theta(i-1)
enddo
+#else
+ if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ iti = itortyp(itype(i-2))
+ else
+ iti=ntortyp+1
+ endif
+c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+ if (i.gt. nnt+1 .and. i.lt.nct+1) then
+ iti1 = itortyp(itype(i-1))
+ else
+ iti1=ntortyp+1
+ endif
+ b1(1,i-2)=b(3,iti)
+ b1(2,i-2)=b(5,iti)
+ b2(1,i-2)=b(2,iti)
+ b2(2,i-2)=b(4,iti)
+ b1tilde(1,i-2)=b1(1,i-2)
+ b1tilde(2,i-2)=-b1(2,i-2)
+ b2tilde(1,i-2)=b2(1,i-2)
+ b2tilde(2,i-2)=-b2(2,i-2)
+ EE(1,2,i-2)=eeold(1,2,iti)
+ EE(2,1,i-2)=eeold(2,1,iti)
+ EE(2,2,i-2)=eeold(2,2,iti)
+ EE(1,1,i-2)=eeold(1,1,iti)
+ enddo
+#endif
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
do i=3,nres+1
#endif
-#endif
if (i .lt. nres+1) then
sin1=dsin(phi(i))
cos1=dcos(phi(i))
do k=1,2
mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1)
enddo
+C write (iout,*) 'mumu',i,b1(1,i-1),Ub2(1,i-2)
c write (iout,*) 'mu ',mu(:,i-2),i-2
cd write (iout,*) 'mu1',mu1(:,i-2)
cd write (iout,*) 'mu2',mu2(:,i-2)
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)
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
c
c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
c
+CTU KURWA
do i=iatel_s,iatel_e
+C do i=75,75
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
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
+C I TU KURWA
do j=ielstart(i),ielend(i)
+C do j=16,17
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
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),
el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
el2=fac4*fac
C MARYSIA
- eesij=(el1+el2)
+C 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
+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
cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
write (iout,'(a6,2i5,0pf7.3,2i5,2e11.3)')
&'evdw1',i,j,evdwij
&,iteli,itelj,aaa,evdw1
- write (iout,'(a6,2i5,0pf7.3)') 'ees',i,j,eesij
+ write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
+ &fac_shield(i),fac_shield(j)
endif
C
erij(1)=xj*rmij
erij(2)=yj*rmij
erij(3)=zj*rmij
+
*
* Radial derivatives. First process both termini of the fragment (i,j)
*
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
+
+C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)
+C gshieldc_loc(k,iresshield)=gshieldc_loc(k,iresshield)
+C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)
+C if (iresshield.gt.j) then
+C do ishi=j+1,iresshield-1
+C gshieldc(k,ishi)=gshieldc(k,ishi)+rlocshield
+C & +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)
+C
+C enddo
+C else
+C do ishi=iresshield,j
+C gshieldc(k,ishi)=gshieldc(k,ishi)-rlocshield
+C & -grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)
+C enddo
+C endif
+ 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
c do k=1,3
c ghalf=0.5D0*ggg(k)
c gelc(k,i)=gelc(k,i)+ghalf
c gelc(k,j)=gelc(k,j)+ghalf
c enddo
c 9/28/08 AL Gradient compotents will be summed only at the end
+C print *,"before", gelc_long(1,i), gelc_long(1,j)
do k=1,3
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
+C & +grad_shield(k,j)*eesij/fac_shield(j)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
+C & +grad_shield(k,i)*eesij/fac_shield(i)
+C gelc_long(k,i-1)=gelc_long(k,i-1)
+C & +grad_shield(k,i)*eesij/fac_shield(i)
+C gelc_long(k,j-1)=gelc_long(k,j-1)
+C & +grad_shield(k,j)*eesij/fac_shield(j)
enddo
+C print *,"bafter", gelc_long(1,i), gelc_long(1,j)
+
*
* Loop over residues i+1 thru j-1.
*
* Radial derivatives. First process both termini of the fragment (i,j)
*
ggg(1)=fac*xj
+C+eesij*grad_shield(1,i)+eesij*grad_shield(1,j)
ggg(2)=fac*yj
+C+eesij*grad_shield(2,i)+eesij*grad_shield(2,j)
ggg(3)=fac*zj
+C+eesij*grad_shield(3,i)+eesij*grad_shield(3,j)
c do k=1,3
c ghalf=0.5D0*ggg(k)
c gelc(k,i)=gelc(k,i)+ghalf
cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
cd & (dcosg(k),k=1,3)
do k=1,3
- ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
+ ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*
+ & fac_shield(i)**2*fac_shield(j)**2
enddo
c do k=1,3
c ghalf=0.5D0*ggg(k)
cgrad gelc(l,k)=gelc(l,k)+ggg(l)
cgrad enddo
cgrad enddo
+C print *,"before22", gelc_long(1,i), gelc_long(1,j)
do k=1,3
gelc(k,i)=gelc(k,i)
- & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
- & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+ & +((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)
- & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
- & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+ & +((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
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
enddo
+C print *,"before33", gelc_long(1,i), gelc_long(1,j)
+
C MARYSIA
c endif !sscale
IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
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 Now derivative over eel_loc
+ 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
+
+
c write (iout,*) 'i',i,' j',j,itype(i),itype(j),
c & ' eel_loc_ij',eel_loc_ij
-c write(iout,*) 'muije=',muij(1),muij(2),muij(3),muij(4)
+C write(iout,*) 'muije=',i,j,muij(1),muij(2),muij(3),muij(4)
C Calculate patrial derivative for theta angle
#ifdef NEWCORR
- geel_loc_ij=a22*gmuij1(1)
+ geel_loc_ij=(a22*gmuij1(1)
& +a23*gmuij1(2)
& +a32*gmuij1(3)
- & +a33*gmuij1(4)
+ & +a33*gmuij1(4))
+ & *fac_shield(i)*fac_shield(j)
c write(iout,*) "derivative over thatai"
c write(iout,*) a22*gmuij1(1), a23*gmuij1(2) ,a32*gmuij1(3),
c & a33*gmuij1(4)
& +a33*gmuij2(4)
gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
& geel_loc_ij*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+
c Derivative over j residue
geel_loc_ji=a22*gmuji1(1)
& +a23*gmuji1(2)
gloc(nphi+j,icg)=gloc(nphi+j,icg)+
& geel_loc_ji*wel_loc
+ & *fac_shield(i)*fac_shield(j)
+
geel_loc_ji=
& +a22*gmuji2(1)
& +a23*gmuji2(2)
c & a33*gmuji2(4)
gloc(nphi+j-1,icg)=gloc(nphi+j-1,icg)+
& geel_loc_ji*wel_loc
+ & *fac_shield(i)*fac_shield(j)
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
C Partial derivatives in virtual-bond dihedral angles gamma
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)
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)
gel_loc_long(l,j)=gel_loc_long(l,j)+ggg(l)
gel_loc_long(l,i)=gel_loc_long(l,i)-ggg(l)
cgrad ghalf=0.5d0*ggg(l)
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))
+ & *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
C Change 12/26/95 to calculate four-body contributions to H-bonding energy
ees0mij=0
endif
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
C Diagnostics. Comment out or remove after debugging!
cdiag do k=1,3
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
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),
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
call matmat2(a_temp(1,1),auxgmatt1(1,1),gpizda1(1,1))
call matmat2(a_temp(1,1),auxgmatt2(1,1),gpizda2(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)
C Derivatives in theta
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3
+ & *fac_shield(i)*fac_shield(j)
gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)
& +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3
+ & *fac_shield(i)*fac_shield(j)
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'eturn3',i,j,0.5d0*(pizda(1,1)+pizda(2,2))
+
+C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+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 if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
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
call transpose2(auxmat2(1,1),auxmat3(1,1))
call matmat2(a_temp(1,1),auxmat3(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),auxmat3(1,1))
call matmat2(a_temp(1,1),auxmat3(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
c ghalf1=0.5d0*agg(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)!+agg(l,1)
a_temp(1,2)=aggi1(l,2)!+agg(l,2)
a_temp(2,1)=aggi1(l,3)!+agg(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)!+ghalf1
a_temp(1,2)=aggj(l,2)!+ghalf2
a_temp(2,1)=aggj(l,3)!+ghalf3
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
return
end
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
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),
gsEE1=0.5d0*(gtEpizda1(1,1)+gtEpizda1(2,2))
gsEE2=0.5d0*(gtEpizda2(1,1)+gtEpizda2(2,2))
gsEE3=0.5d0*(gtEpizda3(1,1)+gtEpizda3(2,2))
-
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+C else
+C fac_shield(i)=0.6
+C fac_shield(j)=0.4
+ 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)
c write(iout,*)'chujOWO', auxvec(1),b1(1,iti2)
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,3f7.3)')
& 'eturn4',i,j,-(s1+s2+s3),s1,s2,s3
+C Now derivative over shield:
+ 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
+
+
+
+
+
+
cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
cd & ' eello_turn4_num',8*eello_turn4_num
#ifdef NEWCORR
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& -(gs13+gsE13+gsEE1)*wturn4
+ & *fac_shield(i)*fac_shield(j)
gloc(nphi+i+1,icg)= gloc(nphi+i+1,icg)
& -(gs23+gs21+gsEE2)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
gloc(nphi+i+2,icg)= gloc(nphi+i+2,icg)
& -(gs32+gsE31+gsEE3)*wturn4
+ & *fac_shield(i)*fac_shield(j)
+
c gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)-
c & gs2
#endif
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(auxmat3(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
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)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
c write (iout,*) "s1",s1," s2",s2," s3",s3," s1+s2+s3",s1+s2+s3
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
+ & *fac_shield(i)*fac_shield(j)
enddo
return
end
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
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
enddo
endif
enddo
- ehpb=0.5D0*ehpb
+ if (constr_dist.ne.11) ehpb=0.5D0*ehpb
return
end
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.
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
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
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),
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
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)
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
enddo
else
phii1=0.0d0
- ityp3=nthetyp+1
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
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)
& 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
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,
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
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)
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
return
end
#endif
+C----------------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine etor_kcc(etors,edihcnstr)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.VAR'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.TORSION'
+ include 'COMMON.INTERACT'
+ include 'COMMON.DERIV'
+ include 'COMMON.CHAIN'
+ include 'COMMON.NAMES'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.FFIELD'
+ include 'COMMON.TORCNSTR'
+ include 'COMMON.CONTROL'
+ logical lprn
+ double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=.false.
+c lprn=.true.
+ etors=0.0D0
+ do i=iphi_start,iphi_end
+C ANY TWO ARE DUMMY ATOMS in row CYCLE
+c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or.
+c & ((itype(i-2).eq.ntyp1).and.(itype(i-1).eq.ntyp1)) .or.
+c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle
+ if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1 .or. itype(i-3).eq.ntyp1) cycle
+ itori=itortyp_kcc(itype(i-2))
+ itori1=itortyp_kcc(itype(i-1))
+ phii=phi(i)
+ glocig=0.0D0
+ glocit1=0.0d0
+ glocit2=0.0d0
+ sumnonchebyshev=0.0d0
+ sumchebyshev=0.0d0
+C to avoid multiple devision by 2
+ theti22=0.5d0*theta(i)
+C theta 12 is the theta_1 /2
+C theta 22 is theta_2 /2
+ theti12=0.5d0*theta(i-1)
+C and appropriate sinus function
+ sinthet2=dsin(theta(i))
+ sinthet1=dsin(theta(i-1))
+ costhet1=dcos(theta(i-1))
+ costhet2=dcos(theta(i))
+C to speed up lets store its mutliplication
+ sint1t2=sinthet2*sinthet1
+C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma)
+C +d_n*sin(n*gamma)) *
+C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2)))
+C we have two sum 1) Non-Chebyshev which is with n and gamma
+ do j=1,nterm_kcc(itori,itori1)
+
+ v1ij=v1_kcc(j,itori,itori1)
+ v2ij=v2_kcc(j,itori,itori1)
+C v1ij is c_n and d_n in euation above
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ sint1t2n=sint1t2**j
+ sumnonchebyshev=sumnonchebyshev+
+ & sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+ actval=sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi)
+C if (energy_dec) etors_ii=etors_ii+
+C & v1ij*cosphi+v2ij*sinphi
+C glocig is the gradient local i site in gamma
+ glocig=glocig+j*(v2ij*cosphi-v1ij*sinphi)*sint1t2n
+C now gradient over theta_1
+ glocit1=glocit1+actval/sinthet1*j*costhet1
+ glocit2=glocit2+actval/sinthet2*j*costhet2
+ enddo
+
+C now the Czebyshev polinominal sum
+ do j=1,nterm_kcc_Tb(itori,itori1)
+ thybt1(j)=v1_chyb(j,itori,itori1)
+ thybt2(j)=v2_chyb(j,itori,itori1)
+ enddo
+ sumth1thyb=tschebyshev
+ & (1,nterm_kcc_Tb(itori,itori1),thybt1(1),dcos(theta12))
+ gradthybt1=gradtschebyshev
+ & (0,nterm_kcc_Tb(itori,itori1)-1,thybt1(1),dcos(theta12))
+ & *(nterm_kcc_Tb(itori,itori1))*0.5*dsin(theta12)
+ sumth2thyb=tschebyshev
+ & (1,nterm_kcc_Tb(itori,itori1),thybt2(1),dcos(theta22))
+ gradthybt2=gradtschebyshev
+ & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),dcos(theta22))
+ & *(nterm_kcc_Tb(itori,itori1))*0.5*dsin(theta22)
+
+C now overal sumation
+ etors=etors+(1.0d0+sumth1thyb+sumth2thyb)*sumnonchebyshev
+C derivative over gamma
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
+ & *(1.0d0+sumth1thyb+sumth2thyb)
+C derivative over theta1
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wang*
+ & (glocit1*(1.0d0+sumth1thyb+sumth2thyb)+
+ & sumnonchebyshev*gradthybt1)
+C now derivative over theta2
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*
+ & (glocit2*(1.0d0+sumth1thyb+sumth2thyb)+
+ & sumnonchebyshev*gradthybt2)
+ enddo
+
+
+C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
+! 6/20/98 - dihedral angle constraints
+ if (tor_mode.ne.2) then
+ edihcnstr=0.0d0
+c do i=1,ndih_constr
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ difi=pinorm(phii-phi0(i))
+ if (difi.gt.drange(i)) then
+ difi=difi-drange(i)
+ 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(i)*difi**4
+ gloc(itori-3,icg)=gloc(itori-3,icg)+ftors(i)*difi**3
+ else
+ difi=0.0
+ endif
+ enddo
+ endif
+ return
+ end
+
+
+
c------------------------------------------------------------------------------
subroutine eback_sc_corr(esccor)
c 7/21/2007 Correlations between the backbone-local and side-chain-local
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
logical lprn
lprn=.false.
include 'COMMON.CONTACTS'
include 'COMMON.CHAIN'
include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
integer num_cont_hb_old(maxres)
logical lprn,ldone
call calc_eello(i,jp,i+1,jp1,jj,kk)
if (wcorr4.gt.0.0d0)
& ecorr=ecorr+eello4(i,jp,i+1,jp1,jj,kk)
+CC & *fac_shield(i)**2*fac_shield(j)**2
if (energy_dec.and.wcorr4.gt.0.0d0)
1 write (iout,'(a6,4i5,0pf7.3)')
2 'ecorr4',i,j,i+1,j1,eello4(i,jp,i+1,jp1,jj,kk)
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
+ include 'COMMON.SHIELD'
+ include 'COMMON.CONTROL'
double precision gx(3),gx1(3)
logical lprn
lprn=.false.
+C print *,"wchodze",fac_shield(i),shield_mode
eij=facont_hb(jj,i)
ekl=facont_hb(kk,k)
ees0pij=ees0p(jj,i)
ees0mkl=ees0m(kk,k)
ekont=eij*ekl
ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl)
+C*
+C & fac_shield(i)**2*fac_shield(j)**2
cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl)
C Following 4 lines for diagnostics.
cd ees0pkl=0.0D0
cgrad enddo
cgrad enddo
c write (iout,*) "ehbcorr",ekont*ees
+C print *,ekont,ees,i,k
ehbcorr=ekont*ees
+C now gradient over shielding
+C return
+ 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
return
end
#ifdef MOMENT
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
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/,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
+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--------------------------------------------------------------------------
+ double precision function tschebyshev(m,n,x,y)
+ implicit none
+ include "DIMENSIONS"
+ integer i,m,n
+ double precision x(n),y,yy(0:maxvar),aux
+c Tschebyshev polynomial. Note that the first term is omitted
+c m=0: the constant term is included
+c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=y
+ do i=2,n
+ yy(i)=2*yy(1)*yy(i-1)-yy(i-2)
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i)*yy(i)
+ enddo
+ tschebyshev=aux
+ return
+ end
+C--------------------------------------------------------------------------
+ double precision function gradtschebyshev(m,n,x,y)
+ implicit none
+ include "DIMENSIONS"
+ integer i,m,n
+ double precision x(n),y,yy(0:maxvar),aux
+c Tschebyshev polynomial. Note that the first term is omitted
+c m=0: the constant term is included
+c m=1: the constant term is not included
+ yy(0)=1.0d0
+ yy(1)=2.0d0*y
+ do i=2,n
+ yy(i)=2*yy(1)*yy(i-1)-yy(i-2)
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i)*yy(i)
+ enddo
+ gradtschebyshev=aux
+ return
+ end
+