subroutine etotal(energia,fact)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
#ifndef ISNAN
external proc_proc
include 'COMMON.IOUNITS'
double precision energia(0:max_ene),energia1(0:max_ene+1)
-#ifdef MPL
- include 'COMMON.INFO'
- external d_vadd
- integer ready
-#endif
include 'COMMON.FFIELD'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
+ include 'COMMON.SHIELD'
+ include 'COMMON.CONTROL'
+ include 'COMMON.TORCNSTR'
double precision fact(6)
-cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot
+c write(iout, '(a,i2)')'Calling etotal ipot=',ipot
+c call flush(iout)
cd print *,'nnt=',nnt,' nct=',nct
C
C Compute the side-chain and electrostatic interaction energy
C
C Calculate electrostatic (H-bonding) energy of the main chain.
C
- 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
-C
+ 106 continue
+c write (iout,*) "Sidechain"
+ call flush(iout)
+ call vec_and_deriv
+ 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 call flush(iout)
+
C Calculate excluded-volume interaction energy between peptide groups
C and side chains.
C
c
c Calculate the bond-stretching energy
c
+
call ebond(estr)
-c write (iout,*) "estr",estr
+C write (iout,*) "estr",estr
C
C Calculate the disulfide-bridge and other energy and the contributions
C from other distance constraints.
C
C Calculate the virtual-bond-angle energy.
C
- call ebend(ebe)
+C print *,'Bend energy finished.'
+ if (wang.gt.0d0) then
+ if (tor_mode.eq.0) then
+ call ebend(ebe)
+ else
+C ebend kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ call ebend_kcc(ebe)
+ endif
+ else
+ ebe=0.0d0
+ endif
+ ethetacnstr=0.0d0
+ if (with_theta_constr) call etheta_constr(ethetacnstr)
+c call ebend(ebe,ethetacnstr)
cd print *,'Bend energy finished.'
C
C Calculate the SC local energy.
C
call esc(escloc)
-cd print *,'SCLOC energy finished.'
+C print *,'SCLOC energy finished.'
C
C Calculate the virtual-bond torsional energy.
C
-cd print *,'nterm=',nterm
- call etor(etors,edihcnstr,fact(1))
+ if (wtor.gt.0.0d0) then
+ if (tor_mode.eq.0) then
+ call etor(etors,fact(1))
+ else
+C etor kcc is Kubo cumulant clustered rigorous attemp to derive the
+C energy function
+ call etor_kcc(etors,fact(1))
+ endif
+ else
+ etors=0.0d0
+ endif
+ edihcnstr=0.0d0
+ if (ndih_constr.gt.0) call etor_constr(edihcnstr)
+c print *,"Processor",myrank," computed Utor"
C
C 6/23/01 Calculate double-torsional energy
C
- call etor_d(etors_d,fact(2))
-C
-C 21/5/07 Calculate local sicdechain correlation energy
+ if ((wtor_d.gt.0.0d0).and.(tor_mode.eq.0)) then
+ call etor_d(etors_d,fact(2))
+ else
+ etors_d=0
+ endif
+c print *,"Processor",myrank," computed Utord"
C
call eback_sc_corr(esccor)
+
+ if (wliptran.gt.0) then
+ call Eliptransfer(eliptran)
+ endif
+
C
C 12/1/95 Multi-body terms
C
n_corr1=0
if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0
& .or. wturn6.gt.0.0d0) then
-c print *,"calling multibody_eello"
+c write(iout,*)"calling multibody_eello"
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
+c write (iout,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
+c write (iout,*) 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
+c write (iout,*) "Calling multibody_hbond"
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
-c call enerprint(energia(0),frac)
#ifdef SCP14
energia(2)=evdw2-evdw2_14
energia(17)=evdw2_14
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
+#ifdef DEBUG
+ call enerprint(energia,fact)
+#endif
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)
- & +wsccor*fact(1)*gsccor_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------------------------------------------------------------------------
subroutine enerprint(energia,fact)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.FFIELD'
include 'COMMON.SBRIDGE'
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
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include "DIMENSIONS.COMPAR"
parameter (accur=1.0d-10)
include 'COMMON.GEO'
integer icant
external icant
cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
+c ROZNICA z cluster
+c do i=1,210
+c do j=1,2
+c eneps_temp(j,i)=0.0d0
+c enddo
+c enddo
+cROZNICA
+
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
cd & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
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
+c eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
+c 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
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
integer icant
external icant
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
+c do i=1,210
+c do j=1,2
+c eneps_temp(j,i)=0.0d0
+c enddo
+c enddo
evdw=0.0D0
evdw_t=0.0d0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
C
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
zj=c(3,nres+j)-zi
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)
+c eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm)
+c & /dabs(eps(itypi,itypj))
+c eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps(itypi,itypj)
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),8(1pd12.4)/2(3(1pd12.4),5x)/)')
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
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
logical lprn
integer icant
external icant
+c do i=1,210
+c do j=1,2
+c eneps_temp(j,i)=0.0d0
+c enddo
+c enddo
evdw=0.0D0
evdw_t=0.0d0
c print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
c endif
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
do iint=1,nint_gr(i)
do j=istart(i,iint),iend(i,iint)
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
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
evdwij=evdwij*eps2rt*eps3rt
ij=icant(itypi,itypj)
aux=eps1*eps2rt**2*eps3rt**2
- if (bb(itypi,itypj).gt.0.0d0) then
+c eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux
+c & /dabs(eps(itypi,itypj))
+c eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj)
+ 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)
-cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
-cd & restyp(itypi),i,restyp(itypj),j,
-cd & epsi,sigm,chi1,chi2,chip1,chip2,
-cd & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
-cd & om1,om2,om12,1.0D0/dsqrt(rrij),
-cd & evdwij
+ 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,
+ & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
+ & om1,om2,om12,1.0D0/dsqrt(rrij),
+ & evdwij
endif
C Calculate gradient components.
e1=e1*eps1*eps2rt**2*eps3rt**2
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include "DIMENSIONS.COMPAR"
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
- integer icant
+ integer icant,xshift,yshift,zshift
external icant
+c do i=1,210
+c do j=1,2
+c eneps_temp(j,i)=0.0d0
+c enddo
+c enddo
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
evdw_t=0.0d0
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+C returning the ith atom to box
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+ if ((zi.gt.bordlipbot)
+ &.and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
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=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+C returning jth atom to box
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C if (aa.ne.aa_aq(itypi,itypj)) 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
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+C finding the closest
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
c write (iout,*) i,j,xj,yj,zj
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
+ 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
- evdw=evdw+evdwij
+ if (bb.gt.0) then
+ evdw=evdw+evdwij*sss
else
- evdw_t=evdw_t+evdwij
+ evdw_t=evdw_t+evdwij*sss
endif
ij=icant(itypi,itypj)
aux=eps1*eps2rt**2*eps3rt**2
+c eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1
+c & /dabs(eps(itypi,itypj))
+c eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
c & aux*e2/eps(itypi,itypj)
c if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
-c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
-c & restyp(itypi),i,restyp(itypj),j,
-c & epsi,sigm,chi1,chi2,chip1,chip2,
-c & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
-c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
-c & evdwij
-c write (iout,*) "pratial sum", evdw,evdw_t
+ 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,
+ & epsi,sigm,chi1,chi2,chip1,chip2,
+ & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
+ & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+ & evdwij
+ write (iout,*) "partial sum", evdw, evdw_t
+#endif
+C#undef DEBUG
c endif
if (calc_grad) then
C Calculate gradient components.
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
fac=rij*fac
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
C Calculate the radial part of the gradient
gg(1)=xj*fac
gg(2)=yj*fac
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
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include "DIMENSIONS.COMPAR"
+ include 'COMMON.CONTROL'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
include 'COMMON.INTERACT'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
+ include 'COMMON.SBRIDGE'
common /srutu/ icall
logical lprn
integer icant
external icant
+c do i=1,210
+c do j=1,2
+c eneps_temp(j,i)=0.0d0
+c enddo
+c enddo
evdw=0.0D0
evdw_t=0.0d0
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
c if (icall.gt.0) lprn=.true.
ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
- if (itypi.eq.21) cycle
- itypi1=itype(i+1)
+ itypi=iabs(itype(i))
+ if (itypi.eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+C returning the ith atom to box
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+ if ((zi.gt.bordlipbot)
+ & .and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+ dxi=dc_norm(1,nres+i)
+ dyi=dc_norm(2,nres+i)
+ dzi=dc_norm(3,nres+i)
+ dsci_inv=vbld_inv(i+nres)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,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
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+ & '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
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3,2f10.3)')
+ & 'evdw',i,j,evdwij,'tss',evdw,evdw_t
+ endif!dyn_ss_mask(k)
+ enddo! k
+ ELSE
ind=ind+1
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
dscj_inv=vbld_inv(j+nres)
sig0ij=sigma(itypi,itypj)
r0ij=r0(itypi,itypj)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+C returning jth atom to box
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ & .and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C if (aa.ne.aa_aq(itypi,itypj)) 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
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+C finding the closest
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if (dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
+c write (iout,*) i,j,xj,yj,zj
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
+ sss=sscale((1.0d0/rij)/sigma(itypi,itypj))
+ sssgrad=sscagrad((1.0d0/rij)/sigma(itypi,itypj))
+ 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
fac_augm=rrij**expon
e_augm=augm(itypi,itypj)*fac_augm
evdwij=evdwij*eps2rt*eps3rt
- if (bb(itypi,itypj).gt.0.0d0) then
- evdw=evdw+evdwij+e_augm
+ if (bb.gt.0) then
+ evdw=evdw+evdwij*sss+e_augm
else
- evdw_t=evdw_t+evdwij+e_augm
+ evdw_t=evdw_t+evdwij*sss+e_augm
endif
+c evdw=evdw+evdwij+e_augm
ij=icant(itypi,itypj)
aux=eps1*eps2rt**2*eps3rt**2
+c eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1
+c & /dabs(eps(itypi,itypj))
+c eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
+c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
+c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
+c & aux*e2/eps(itypi,itypj)
c if (lprn) then
-c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
-c epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
-c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
-c & restyp(itypi),i,restyp(itypj),j,
-c & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
-c & chi1,chi2,chip1,chip2,
-c & eps1,eps2rt**2,eps3rt**2,
-c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
-c & evdwij+e_augm
+c#define DEBUG
+#ifdef DEBUG
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
+ write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+ & restyp(itypi),i,restyp(itypj),j,
+ & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
+ & chi1,chi2,chip1,chip2,
+ & eps1,eps2rt**2,eps3rt**2,
+ & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+ & evdwij+e_augm
+ write (iout,*) "partial sum", evdw, evdw_t
+#endif
+c#undef DEBUG
c endif
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+ & 'evdw',i,j,evdwij
if (calc_grad) then
C Calculate gradient components.
e1=e1*eps1*eps2rt**2*eps3rt**2
fac=-expon*(e1+evdwij)*rij_shift
sigder=fac*sigder
- fac=rij*fac-2*expon*rrij*e_augm
+ fac=rij*fac
+ fac=fac+evdwij/sss*sssgrad/sigma(itypi,itypj)*rij
C Calculate the radial part of the gradient
gg(1)=xj*fac
gg(2)=yj*fac
C Calculate angular part of the gradient.
call sc_grad
endif
+ ENDIF
enddo ! j
enddo ! iint
enddo ! i
subroutine sc_grad
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.CALC'
subroutine vec_and_deriv
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.VAR'
call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
costh=dcos(pi-theta(nres))
fac=1.0d0/dsqrt(1.0d0-costh*costh)
+c write (iout,*) "i",i," dc_norm",dc_norm(:,i),dc_norm(:,i-1),
+c & " uz",uz(:,i)
do k=1,3
uz(k,i)=fac*uz(k,i)
enddo
uzder(1,3,2)= dc_norm(2,i)
uzder(2,3,2)=-dc_norm(1,i)
uzder(3,3,2)= 0.0d0
- endif
+ endif ! calc_grad
C Compute the Y-axis
facy=fac
do k=1,3
endif
return
end
-C-----------------------------------------------------------------------------
- subroutine vec_and_deriv_test
+C--------------------------------------------------------------------------
+ subroutine set_matrices
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
+#ifdef MPI
+ include "mpif.h"
+ integer IERR
+ integer status(MPI_STATUS_SIZE)
+#endif
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
include 'COMMON.CHAIN'
- include 'COMMON.VECTORS'
- dimension uyder(3,3,2),uzder(3,3,2)
-C Compute the local reference systems. For reference system (i), the
-C X-axis points from CA(i) to CA(i+1), the Y axis is in the
-C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
- do i=1,nres-1
- if (i.eq.nres-1) then
-C Case of the last full residue
-C Compute the Z-axis
- call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
- costh=dcos(pi-theta(nres))
- fac=1.0d0/dsqrt(1.0d0-costh*costh)
-c write (iout,*) 'fac',fac,
-c & 1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
- fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
- do k=1,3
- uz(k,i)=fac*uz(k,i)
- enddo
-C Compute the derivatives of uz
- uzder(1,1,1)= 0.0d0
- uzder(2,1,1)=-dc_norm(3,i-1)
- uzder(3,1,1)= dc_norm(2,i-1)
- uzder(1,2,1)= dc_norm(3,i-1)
- uzder(2,2,1)= 0.0d0
- uzder(3,2,1)=-dc_norm(1,i-1)
- uzder(1,3,1)=-dc_norm(2,i-1)
- uzder(2,3,1)= dc_norm(1,i-1)
- uzder(3,3,1)= 0.0d0
- uzder(1,1,2)= 0.0d0
- uzder(2,1,2)= dc_norm(3,i)
- uzder(3,1,2)=-dc_norm(2,i)
- uzder(1,2,2)=-dc_norm(3,i)
- uzder(2,2,2)= 0.0d0
- uzder(3,2,2)= dc_norm(1,i)
- uzder(1,3,2)= dc_norm(2,i)
- uzder(2,3,2)=-dc_norm(1,i)
- uzder(3,3,2)= 0.0d0
-C Compute the Y-axis
- do k=1,3
- uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
- enddo
- facy=fac
- facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
- & (scalar(dc_norm(1,i-1),dc_norm(1,i-1))**2-
- & scalar(dc_norm(1,i),dc_norm(1,i-1))**2))
- do k=1,3
-c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
- uy(k,i)=
-c & facy*(
- & dc_norm(k,i-1)*scalar(dc_norm(1,i),dc_norm(1,i))
- & -scalar(dc_norm(1,i),dc_norm(1,i-1))*dc_norm(k,i)
-c & )
- enddo
-c write (iout,*) 'facy',facy,
-c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
- facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
- do k=1,3
- uy(k,i)=facy*uy(k,i)
- enddo
-C Compute the derivatives of uy
- do j=1,3
- do k=1,3
- uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
- & -dc_norm(k,i)*dc_norm(j,i-1)
- uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
- enddo
-c uyder(j,j,1)=uyder(j,j,1)-costh
-c uyder(j,j,2)=1.0d0+uyder(j,j,2)
- uyder(j,j,1)=uyder(j,j,1)
- & -scalar(dc_norm(1,i),dc_norm(1,i-1))
- uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
- & +uyder(j,j,2)
- enddo
- do j=1,2
- do k=1,3
- do l=1,3
- uygrad(l,k,j,i)=uyder(l,k,j)
- uzgrad(l,k,j,i)=uzder(l,k,j)
- enddo
- enddo
- enddo
- call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
- call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
- call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
- call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
- else
-C Other residues
-C Compute the Z-axis
- call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
- costh=dcos(pi-theta(i+2))
- fac=1.0d0/dsqrt(1.0d0-costh*costh)
- fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
- do k=1,3
- uz(k,i)=fac*uz(k,i)
- enddo
-C Compute the derivatives of uz
- uzder(1,1,1)= 0.0d0
- uzder(2,1,1)=-dc_norm(3,i+1)
- uzder(3,1,1)= dc_norm(2,i+1)
- uzder(1,2,1)= dc_norm(3,i+1)
- uzder(2,2,1)= 0.0d0
- uzder(3,2,1)=-dc_norm(1,i+1)
- uzder(1,3,1)=-dc_norm(2,i+1)
- uzder(2,3,1)= dc_norm(1,i+1)
- uzder(3,3,1)= 0.0d0
- uzder(1,1,2)= 0.0d0
- uzder(2,1,2)= dc_norm(3,i)
- uzder(3,1,2)=-dc_norm(2,i)
- uzder(1,2,2)=-dc_norm(3,i)
- uzder(2,2,2)= 0.0d0
- uzder(3,2,2)= dc_norm(1,i)
- uzder(1,3,2)= dc_norm(2,i)
- uzder(2,3,2)=-dc_norm(1,i)
- uzder(3,3,2)= 0.0d0
-C Compute the Y-axis
- facy=fac
- facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
- & (scalar(dc_norm(1,i+1),dc_norm(1,i+1))**2-
- & scalar(dc_norm(1,i),dc_norm(1,i+1))**2))
- do k=1,3
-c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
- uy(k,i)=
-c & facy*(
- & dc_norm(k,i+1)*scalar(dc_norm(1,i),dc_norm(1,i))
- & -scalar(dc_norm(1,i),dc_norm(1,i+1))*dc_norm(k,i)
-c & )
- enddo
-c write (iout,*) 'facy',facy,
-c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
- facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
- do k=1,3
- uy(k,i)=facy*uy(k,i)
- enddo
-C Compute the derivatives of uy
- do j=1,3
- do k=1,3
- uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
- & -dc_norm(k,i)*dc_norm(j,i+1)
- uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
- enddo
-c uyder(j,j,1)=uyder(j,j,1)-costh
-c uyder(j,j,2)=1.0d0+uyder(j,j,2)
- uyder(j,j,1)=uyder(j,j,1)
- & -scalar(dc_norm(1,i),dc_norm(1,i+1))
- uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
- & +uyder(j,j,2)
- enddo
- do j=1,2
- do k=1,3
- do l=1,3
- uygrad(l,k,j,i)=uyder(l,k,j)
- uzgrad(l,k,j,i)=uzder(l,k,j)
- enddo
- enddo
- enddo
- call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
- call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
- call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
- call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
- endif
- enddo
- do i=1,nres-1
- do j=1,2
- do k=1,3
- do l=1,3
- uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i)
- uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i)
- enddo
- enddo
- enddo
- enddo
- return
- end
-C-----------------------------------------------------------------------------
- subroutine check_vecgrad
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'sizesclu.dat'
- include 'COMMON.IOUNITS'
- include 'COMMON.GEO'
- include 'COMMON.VAR'
- include 'COMMON.LOCAL'
- include 'COMMON.CHAIN'
- include 'COMMON.VECTORS'
- dimension uygradt(3,3,2,maxres),uzgradt(3,3,2,maxres)
- dimension uyt(3,maxres),uzt(3,maxres)
- dimension uygradn(3,3,2),uzgradn(3,3,2),erij(3)
- double precision delta /1.0d-7/
- call vec_and_deriv
-cd do i=1,nres
-crc write(iout,'(2i5,2(3f10.5,5x))') i,1,dc_norm(:,i)
-crc write(iout,'(2i5,2(3f10.5,5x))') i,2,uy(:,i)
-crc write(iout,'(2i5,2(3f10.5,5x)/)')i,3,uz(:,i)
-cd write(iout,'(2i5,2(3f10.5,5x))') i,1,
-cd & (dc_norm(if90,i),if90=1,3)
-cd write(iout,'(2i5,2(3f10.5,5x))') i,2,(uy(if90,i),if90=1,3)
-cd write(iout,'(2i5,2(3f10.5,5x)/)')i,3,(uz(if90,i),if90=1,3)
-cd write(iout,'(a)')
-cd enddo
- do i=1,nres
- do j=1,2
- do k=1,3
- do l=1,3
- uygradt(l,k,j,i)=uygrad(l,k,j,i)
- uzgradt(l,k,j,i)=uzgrad(l,k,j,i)
- enddo
- enddo
- enddo
- enddo
- call vec_and_deriv
- do i=1,nres
- do j=1,3
- uyt(j,i)=uy(j,i)
- uzt(j,i)=uz(j,i)
- enddo
- enddo
- do i=1,nres
-cd write (iout,*) 'i=',i
- do k=1,3
- erij(k)=dc_norm(k,i)
- enddo
- do j=1,3
- do k=1,3
- dc_norm(k,i)=erij(k)
- enddo
- dc_norm(j,i)=dc_norm(j,i)+delta
-c fac=dsqrt(scalar(dc_norm(1,i),dc_norm(1,i)))
-c do k=1,3
-c dc_norm(k,i)=dc_norm(k,i)/fac
-c enddo
-c write (iout,*) (dc_norm(k,i),k=1,3)
-c write (iout,*) (erij(k),k=1,3)
- call vec_and_deriv
- do k=1,3
- uygradn(k,j,1)=(uy(k,i)-uyt(k,i))/delta
- uygradn(k,j,2)=(uy(k,i-1)-uyt(k,i-1))/delta
- uzgradn(k,j,1)=(uz(k,i)-uzt(k,i))/delta
- uzgradn(k,j,2)=(uz(k,i-1)-uzt(k,i-1))/delta
- enddo
-c write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
-c & j,(uzgradt(k,j,1,i),k=1,3),(uzgradn(k,j,1),k=1,3),
-c & (uzgradt(k,j,2,i-1),k=1,3),(uzgradn(k,j,2),k=1,3)
- enddo
- do k=1,3
- dc_norm(k,i)=erij(k)
- enddo
-cd do k=1,3
-cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
-cd & k,(uygradt(k,l,1,i),l=1,3),(uygradn(k,l,1),l=1,3),
-cd & (uygradt(k,l,2,i-1),l=1,3),(uygradn(k,l,2),l=1,3)
-cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
-cd & k,(uzgradt(k,l,1,i),l=1,3),(uzgradn(k,l,1),l=1,3),
-cd & (uzgradt(k,l,2,i-1),l=1,3),(uzgradn(k,l,2),l=1,3)
-cd write (iout,'(a)')
-cd enddo
- enddo
- return
- end
-C--------------------------------------------------------------------------
- subroutine set_matrices
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'sizesclu.dat'
- include 'COMMON.IOUNITS'
- include 'COMMON.GEO'
- include 'COMMON.VAR'
- include 'COMMON.LOCAL'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.INTERACT'
- include 'COMMON.CONTACTS'
- include 'COMMON.TORSION'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
double precision auxvec(2),auxmat(2,2)
C Compute the virtual-bond-torsional-angle dependent quantities needed
C to calculate the el-loc multibody terms of various order.
C
+c write(iout,*) 'SET_MATRICES nphi=',nphi,nres
+ do i=3,nres+1
+ if (i.gt. nnt+2 .and. i.lt.nct+2) then
+ iti = itype2loc(itype(i-2))
+ else
+ iti=nloctyp
+ 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 = itype2loc(itype(i-1))
+ else
+ iti1=nloctyp
+ endif
+#ifdef NEWCORR
+ cost1=dcos(theta(i-1))
+ sint1=dsin(theta(i-1))
+ sint1sq=sint1*sint1
+ sint1cub=sint1sq*sint1
+ sint1cost1=2*sint1*cost1
+#ifdef DEBUG
+ write (iout,*) "bnew1",i,iti
+ write (iout,*) (bnew1(k,1,iti),k=1,3)
+ write (iout,*) (bnew1(k,2,iti),k=1,3)
+ write (iout,*) "bnew2",i,iti
+ write (iout,*) (bnew2(k,1,iti),k=1,3)
+ write (iout,*) (bnew2(k,2,iti),k=1,3)
+#endif
+ do k=1,2
+ b1k=bnew1(1,k,iti)+(bnew1(2,k,iti)+bnew1(3,k,iti)*cost1)*cost1
+ b1(k,i-2)=sint1*b1k
+ gtb1(k,i-2)=cost1*b1k-sint1sq*
+ & (bnew1(2,k,iti)+2*bnew1(3,k,iti)*cost1)
+ b2k=bnew2(1,k,iti)+(bnew2(2,k,iti)+bnew2(3,k,iti)*cost1)*cost1
+ b2(k,i-2)=sint1*b2k
+ if (calc_grad) gtb2(k,i-2)=cost1*b2k-sint1sq*
+ & (bnew2(2,k,iti)+2*bnew2(3,k,iti)*cost1)
+ enddo
+ do k=1,2
+ aux=ccnew(1,k,iti)+(ccnew(2,k,iti)+ccnew(3,k,iti)*cost1)*cost1
+ cc(1,k,i-2)=sint1sq*aux
+ if (calc_grad) gtcc(1,k,i-2)=sint1cost1*aux-sint1cub*
+ & (ccnew(2,k,iti)+2*ccnew(3,k,iti)*cost1)
+ aux=ddnew(1,k,iti)+(ddnew(2,k,iti)+ddnew(3,k,iti)*cost1)*cost1
+ dd(1,k,i-2)=sint1sq*aux
+ if (calc_grad) gtdd(1,k,i-2)=sint1cost1*aux-sint1cub*
+ & (ddnew(2,k,iti)+2*ddnew(3,k,iti)*cost1)
+ enddo
+ cc(2,1,i-2)=cc(1,2,i-2)
+ cc(2,2,i-2)=-cc(1,1,i-2)
+ gtcc(2,1,i-2)=gtcc(1,2,i-2)
+ gtcc(2,2,i-2)=-gtcc(1,1,i-2)
+ dd(2,1,i-2)=dd(1,2,i-2)
+ dd(2,2,i-2)=-dd(1,1,i-2)
+ gtdd(2,1,i-2)=gtdd(1,2,i-2)
+ gtdd(2,2,i-2)=-gtdd(1,1,i-2)
+ do k=1,2
+ do l=1,2
+ aux=eenew(1,l,k,iti)+eenew(2,l,k,iti)*cost1
+ EE(l,k,i-2)=sint1sq*aux
+ if (calc_grad)
+ & gtEE(l,k,i-2)=sint1cost1*aux-sint1cub*eenew(2,l,k,iti)
+ enddo
+ enddo
+ EE(1,1,i-2)=EE(1,1,i-2)+e0new(1,iti)*cost1
+ EE(1,2,i-2)=EE(1,2,i-2)+e0new(2,iti)+e0new(3,iti)*cost1
+ EE(2,1,i-2)=EE(2,1,i-2)+e0new(2,iti)*cost1+e0new(3,iti)
+ EE(2,2,i-2)=EE(2,2,i-2)-e0new(1,iti)
+ if (calc_grad) then
+ gtEE(1,1,i-2)=gtEE(1,1,i-2)-e0new(1,iti)*sint1
+ gtEE(1,2,i-2)=gtEE(1,2,i-2)-e0new(3,iti)*sint1
+ gtEE(2,1,i-2)=gtEE(2,1,i-2)-e0new(2,iti)*sint1
+ endif
+c b1tilde(1,i-2)=b1(1,i-2)
+c b1tilde(2,i-2)=-b1(2,i-2)
+c b2tilde(1,i-2)=b2(1,i-2)
+c b2tilde(2,i-2)=-b2(2,i-2)
+#ifdef DEBUG
+ write (iout,*) 'i=',i-2,gtb1(2,i-2),gtb1(1,i-2)
+ write(iout,*) 'b1=',(b1(k,i-2),k=1,2)
+ write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
+ write (iout,*) 'theta=', theta(i-1)
+#endif
+#else
+c if (i.gt. nnt+2 .and. i.lt.nct+2) then
+c iti = itype2loc(itype(i-2))
+c else
+c iti=nloctyp
+c endif
+c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
+c if (i.gt. nnt+1 .and. i.lt.nct+1) then
+c iti1 = itype2loc(itype(i-1))
+c else
+c iti1=nloctyp
+c 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)
+ do k=1,2
+ do l=1,2
+ CC(k,l,i-2)=ccold(k,l,iti)
+ DD(k,l,i-2)=ddold(k,l,iti)
+ EE(k,l,i-2)=eeold(k,l,iti)
+ enddo
+ enddo
+#endif
+ 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)
+c
+ Ctilde(1,1,i-2)= CC(1,1,i-2)
+ Ctilde(1,2,i-2)= CC(1,2,i-2)
+ Ctilde(2,1,i-2)=-CC(2,1,i-2)
+ Ctilde(2,2,i-2)=-CC(2,2,i-2)
+c
+ Dtilde(1,1,i-2)= DD(1,1,i-2)
+ Dtilde(1,2,i-2)= DD(1,2,i-2)
+ Dtilde(2,1,i-2)=-DD(2,1,i-2)
+ Dtilde(2,2,i-2)=-DD(2,2,i-2)
+c write(iout,*) "i",i," iti",iti
+c write(iout,*) 'b1=',(b1(k,i-2),k=1,2)
+c write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
+ enddo
do i=3,nres+1
if (i .lt. nres+1) then
sin1=dsin(phi(i))
Ug2der(2,1,i-2)=0.0d0
Ug2der(2,2,i-2)=0.0d0
endif
+c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- if (itype(i-2).le.ntyp) then
- iti = itortyp(itype(i-2))
- else
- iti=ntortyp+1
- endif
+ iti = itype2loc(itype(i-2))
else
- iti=ntortyp+1
+ iti=nloctyp
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
- if (itype(i-1).le.ntyp) then
- iti1 = itortyp(itype(i-1))
- else
- iti1=ntortyp+1
- endif
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
cd write (iout,*) '*******i',i,' iti1',iti
cd write (iout,*) 'b1',b1(:,iti)
cd write (iout,*) 'b2',b2(:,iti)
cd write (iout,*) 'Ug',Ug(:,:,i-2)
-c print *,"itilde1 i iti iti1",i,iti,iti1
- if (i .gt. iatel_s+2) then
- call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2))
- call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2))
- call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2))
- call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2))
- call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2))
- call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2))
- call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2))
+c if (i .gt. iatel_s+2) then
+ if (i .gt. nnt+2) then
+ call matvec2(Ug(1,1,i-2),b2(1,i-2),Ub2(1,i-2))
+#ifdef NEWCORR
+ call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2))
+c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj"
+#endif
+c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i),
+c & EE(1,2,iti),EE(2,2,i)
+ call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2))
+ call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2))
+c write(iout,*) "Macierz EUG",
+c & eug(1,1,i-2),eug(1,2,i-2),eug(2,1,i-2),
+c & eug(2,2,i-2)
+ if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0)
+ & then
+ call matmat2(CC(1,1,i-2),Ug(1,1,i-2),CUg(1,1,i-2))
+ call matmat2(DD(1,1,i-2),Ug(1,1,i-2),DUg(1,1,i-2))
+ call matmat2(Dtilde(1,1,i-2),Ug2(1,1,i-2),DtUg2(1,1,i-2))
+ call matvec2(Ctilde(1,1,i-1),obrot(1,i-2),Ctobr(1,i-2))
+ call matvec2(Dtilde(1,1,i-2),obrot2(1,i-2),Dtobr2(1,i-2))
+ endif
else
do k=1,2
Ub2(k,i-2)=0.0d0
enddo
enddo
endif
-c print *,"itilde2 i iti iti1",i,iti,iti1
- call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2))
- call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2))
- call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2))
- call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2))
- call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
- call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2))
- call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2))
-c print *,"itilde3 i iti iti1",i,iti,iti1
+ call matvec2(Ugder(1,1,i-2),b2(1,i-2),Ub2der(1,i-2))
+ call matmat2(EE(1,1,i-2),Ugder(1,1,i-2),EUgder(1,1,i-2))
do k=1,2
muder(k,i-2)=Ub2der(k,i-2)
enddo
+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
if (itype(i-1).le.ntyp) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itype2loc(itype(i-1))
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
else
- iti1=ntortyp+1
+ iti1=nloctyp
endif
do k=1,2
- mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
+ mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1)
enddo
+#ifdef MUOUT
+ write (iout,'(2hmu,i3,3f8.1,12f10.5)') i-2,rad2deg*theta(i-1),
+ & rad2deg*theta(i),rad2deg*phi(i),mu(1,i-2),mu(2,i-2),
+ & -b2(1,i-2),b2(2,i-2),b1(1,i-2),b1(2,i-2),
+ & dsqrt(b2(1,i-1)**2+b2(2,i-1)**2)
+ & +dsqrt(b1(1,i-1)**2+b1(2,i-1)**2),
+ & ((ee(l,k,i-2),l=1,2),k=1,2)
+#endif
+cd write (iout,*) 'mu1',mu1(:,i-2)
+cd write (iout,*) 'mu2',mu2(:,i-2)
+ if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
+ & then
+ if (calc_grad) then
+ call matmat2(CC(1,1,i-1),Ugder(1,1,i-2),CUgder(1,1,i-2))
+ call matmat2(DD(1,1,i-2),Ugder(1,1,i-2),DUgder(1,1,i-2))
+ call matmat2(Dtilde(1,1,i-2),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
+ call matvec2(Ctilde(1,1,i-1),obrot_der(1,i-2),Ctobrder(1,i-2))
+ call matvec2(Dtilde(1,1,i-2),obrot2_der(1,i-2),Dtobr2der(1,i-2))
+ endif
C Vectors and matrices dependent on a single virtual-bond dihedral.
- call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
+ call matvec2(DD(1,1,i-2),b1tilde(1,i-1),auxvec(1))
call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
+ call matvec2(CC(1,1,i-1),Ub2(1,i-2),CUgb2(1,i-2))
+ call matmat2(EUg(1,1,i-2),CC(1,1,i-1),EUgC(1,1,i-2))
+ call matmat2(EUg(1,1,i-2),DD(1,1,i-1),EUgD(1,1,i-2))
+ if (calc_grad) then
call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2))
- call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2))
- call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2))
- call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2))
- call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2))
- call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2))
- call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2))
-cd write (iout,*) 'i',i,' mu ',(mu(k,i-2),k=1,2),
-cd & ' mu1',(b1(k,i-2),k=1,2),' mu2',(Ub2(k,i-2),k=1,2)
+ call matvec2(CC(1,1,i-1),Ub2der(1,i-2),CUgb2der(1,i-2))
+ call matmat2(EUgder(1,1,i-2),CC(1,1,i-1),EUgCder(1,1,i-2))
+ call matmat2(EUgder(1,1,i-2),DD(1,1,i-1),EUgDder(1,1,i-2))
+ endif
+ endif
enddo
C Matrices dependent on two consecutive virtual-bond dihedrals.
C The order of matrices is from left to right.
+ if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0)
+ &then
do i=2,nres-1
call matmat2(DtUg2(1,1,i-1),EUg(1,1,i),DtUg2EUg(1,1,i))
+ if (calc_grad) then
call matmat2(DtUg2der(1,1,i-1),EUg(1,1,i),DtUg2EUgder(1,1,1,i))
call matmat2(DtUg2(1,1,i-1),EUgder(1,1,i),DtUg2EUgder(1,1,2,i))
+ endif
call transpose2(DtUg2(1,1,i-1),auxmat(1,1))
call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUg(1,1,i))
+ if (calc_grad) then
call matmat2(auxmat(1,1),EUgder(1,1,i),Ug2DtEUgder(1,1,2,i))
call transpose2(DtUg2der(1,1,i-1),auxmat(1,1))
call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i))
+ endif
enddo
-cd do i=1,nres
-cd iti = itortyp(itype(i))
-cd write (iout,*) i
-cd do j=1,2
-cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
-cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
-cd enddo
-cd enddo
+ endif
return
end
C--------------------------------------------------------------------------
C the orientation of the CA-CA virtual bonds.
C
implicit real*8 (a-h,o-z)
+#ifdef MPI
+ include 'mpif.h'
+#endif
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.CONTROL'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.TORSION'
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
+ include 'COMMON.TIME1'
+ include 'COMMON.SPLITELE'
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),
- & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
- common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij(4)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
+ & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
+ & num_conti,j1,j2
c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
+#ifdef MOMENT
+ double precision scal_el /1.0d0/
+#else
double precision scal_el /0.5d0/
+#endif
C 12/13/98
C 13-go grudnia roku pamietnego...
double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
& .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or.
& wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then
-cd if (wel_loc.gt.0.0d0) then
- if (icheckgrad.eq.1) then
- call vec_and_deriv_test
- else
- call vec_and_deriv
- endif
+c call vec_and_deriv
+#ifdef TIMING
+ time01=MPI_Wtime()
+#endif
call set_matrices
+#ifdef TIMING
+ time_mat=time_mat+MPI_Wtime()-time01
+#endif
endif
cd do i=1,nres-1
cd write (iout,*) 'i=',i
cd do k=1,3
-cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i)
+cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i)
cd enddo
cd do k=1,3
cd write (iout,'(f10.5,2x,3f10.5,2x,3f10.5)')
cd & uz(k,i),(uzgrad(k,l,1,i),l=1,3),(uzgrad(k,l,2,i),l=1,3)
cd enddo
cd enddo
- num_conti_hb=0
+ t_eelecij=0.0d0
ees=0.0D0
evdw1=0.0D0
eel_loc=0.0d0
num_cont_hb(i)=0
enddo
cd print '(a)','Enter EELEC'
-cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
+c write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
+c call flush(iout)
do i=1,nres
gel_loc_loc(i)=0.0d0
gcorr_loc(i)=0.0d0
enddo
- do i=iatel_s,iatel_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
- if (itel(i).eq.0) goto 1215
+c
+c
+c 9/27/08 AL Split the interaction loop to ensure load balancing of turn terms
+C
+C Loop over i,i+2 and i,i+3 pairs of the peptide groups
+C
+C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
+ do i=iturn3_start,iturn3_end
+c 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
+C Adam: Unnecessary: handled by iturn3_end and iturn3_start
+c & .or.((i+4).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes by Ana
+C dobra zmiana wycofana
+ & .or. itype(i+2).eq.ntyp1
+ & .or. itype(i+3).eq.ntyp1) cycle
+C Adam: Instructions below will switch off existing interactions
+c if(i.gt.1)then
+c if(itype(i-1).eq.ntyp1)cycle
+c end if
+c if(i.LT.nres-3)then
+c if (itype(i+4).eq.ntyp1) cycle
+c end if
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
num_conti=0
+ call eelecij(i,i+2,ees,evdw1,eel_loc)
+ if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
+ num_cont_hb(i)=num_conti
+ enddo
+ do i=iturn4_start,iturn4_end
+ if (i.lt.1) cycle
+ 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
+c & .or. itype(i).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
+ & ) cycle
+ dxi=dc(1,i)
+ dyi=dc(2,i)
+ dzi=dc(3,i)
+ dx_normi=dc_norm(1,i)
+ dy_normi=dc_norm(2,i)
+ dz_normi=dc_norm(3,i)
+ xmedi=c(1,i)+0.5d0*dxi
+ ymedi=c(2,i)+0.5d0*dyi
+ zmedi=c(3,i)+0.5d0*dzi
+C Return atom into box, boxxsize is size of box in x dimension
+c 194 continue
+c if (xmedi.gt.((0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
+c if (xmedi.lt.((-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
+C Condition for being inside the proper box
+c if ((xmedi.gt.((0.5d0)*boxxsize)).or.
+c & (xmedi.lt.((-0.5d0)*boxxsize))) then
+c go to 194
+c endif
+c 195 continue
+c if (ymedi.gt.((0.5d0)*boxysize)) ymedi=ymedi-boxysize
+c if (ymedi.lt.((-0.5d0)*boxysize)) ymedi=ymedi+boxysize
+C Condition for being inside the proper box
+c if ((ymedi.gt.((0.5d0)*boxysize)).or.
+c & (ymedi.lt.((-0.5d0)*boxysize))) then
+c go to 195
+c endif
+c 196 continue
+c if (zmedi.gt.((0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
+c if (zmedi.lt.((-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
+C Condition for being inside the proper box
+c if ((zmedi.gt.((0.5d0)*boxzsize)).or.
+c & (zmedi.lt.((-0.5d0)*boxzsize))) then
+c go to 196
+c endif
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
+
+ num_conti=num_cont_hb(i)
+c write(iout,*) "JESTEM W PETLI"
+ call eelecij(i,i+3,ees,evdw1,eel_loc)
+ if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1)
+ & call eturn4(i,eello_turn4)
+ num_cont_hb(i)=num_conti
+ enddo ! i
+C Loop over all neighbouring boxes
+C do xshift=-1,1
+C do yshift=-1,1
+C do zshift=-1,1
+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
+c 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
+c & .or.((i+2).gt.nres)
+c & .or.((i-1).le.0)
+C end of changes by Ana
+c & .or. itype(i+2).eq.ntyp1
+c & .or. itype(i-1).eq.ntyp1
+ & ) cycle
+ dxi=dc(1,i)
+ dyi=dc(2,i)
+ dzi=dc(3,i)
+ dx_normi=dc_norm(1,i)
+ dy_normi=dc_norm(2,i)
+ dz_normi=dc_norm(3,i)
+ xmedi=c(1,i)+0.5d0*dxi
+ ymedi=c(2,i)+0.5d0*dyi
+ zmedi=c(3,i)+0.5d0*dzi
+ xmedi=mod(xmedi,boxxsize)
+ if (xmedi.lt.0) xmedi=xmedi+boxxsize
+ ymedi=mod(ymedi,boxysize)
+ if (ymedi.lt.0) ymedi=ymedi+boxysize
+ zmedi=mod(zmedi,boxzsize)
+ if (zmedi.lt.0) zmedi=zmedi+boxzsize
+C xmedi=xmedi+xshift*boxxsize
+C ymedi=ymedi+yshift*boxysize
+C zmedi=zmedi+zshift*boxzsize
+
+C Return tom into box, boxxsize is size of box in x dimension
+c 164 continue
+c if (xmedi.gt.((xshift+0.5d0)*boxxsize)) xmedi=xmedi-boxxsize
+c if (xmedi.lt.((xshift-0.5d0)*boxxsize)) xmedi=xmedi+boxxsize
+C Condition for being inside the proper box
+c if ((xmedi.gt.((xshift+0.5d0)*boxxsize)).or.
+c & (xmedi.lt.((xshift-0.5d0)*boxxsize))) then
+c go to 164
+c endif
+c 165 continue
+c if (ymedi.gt.((yshift+0.5d0)*boxysize)) ymedi=ymedi-boxysize
+c if (ymedi.lt.((yshift-0.5d0)*boxysize)) ymedi=ymedi+boxysize
+C Condition for being inside the proper box
+c if ((ymedi.gt.((yshift+0.5d0)*boxysize)).or.
+c & (ymedi.lt.((yshift-0.5d0)*boxysize))) then
+c go to 165
+c endif
+c 166 continue
+c if (zmedi.gt.((zshift+0.5d0)*boxzsize)) zmedi=zmedi-boxzsize
+c if (zmedi.lt.((zshift-0.5d0)*boxzsize)) zmedi=zmedi+boxzsize
+cC Condition for being inside the proper box
+c if ((zmedi.gt.((zshift+0.5d0)*boxzsize)).or.
+c & (zmedi.lt.((zshift-0.5d0)*boxzsize))) then
+c go to 166
+c endif
+
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)
- if (itype(j).eq.21 .or. itype(j+1).eq.21) cycle
- if (itel(j).eq.0) goto 1216
- ind=ind+1
+C do j=16,17
+C write (iout,*) i,j
+C 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
+c & .or.((j+2).gt.nres)
+c & .or.((j-1).le.0)
+C end of changes by Ana
+c & .or.itype(j+2).eq.ntyp1
+c & .or.itype(j-1).eq.ntyp1
+ &) cycle
+ call eelecij(i,j,ees,evdw1,eel_loc)
+ enddo ! j
+ num_cont_hb(i)=num_conti
+ enddo ! i
+C enddo ! zshift
+C enddo ! yshift
+C enddo ! xshift
+
+c write (iout,*) "Number of loop steps in EELEC:",ind
+cd do i=1,nres
+cd write (iout,'(i3,3f10.5,5x,3f10.5)')
+cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i)
+cd enddo
+c 12/7/99 Adam eello_turn3 will be considered as a separate energy term
+ccc eel_loc=eel_loc+eello_turn3
+cd print *,"Processor",fg_rank," t_eelecij",t_eelecij
+ return
+ end
+C-------------------------------------------------------------------------------
+ subroutine eelecij(i,j,ees,evdw1,eel_loc)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include "mpif.h"
+#endif
+ include 'COMMON.CONTROL'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ include 'COMMON.VECTORS'
+ 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),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),gmuij1(4),gmuji1(4),
+ & gmuij2(4),gmuji2(4)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
+ & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
+ & num_conti,j1,j2
+c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
+#ifdef MOMENT
+ double precision scal_el /1.0d0/
+#else
+ double precision scal_el /0.5d0/
+#endif
+C 12/13/98
+C 13-go grudnia roku pamietnego...
+ double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
+ & 0.0d0,1.0d0,0.0d0,
+ & 0.0d0,0.0d0,1.0d0/
+ integer xshift,yshift,zshift
+c time00=MPI_Wtime()
+cd write (iout,*) "eelecij",i,j
+c ind=ind+1
iteli=itel(i)
itelj=itel(j)
if (j.eq.i+2 .and. itelj.eq.2) iteli=2
aaa=app(iteli,itelj)
bbb=bpp(iteli,itelj)
-C Diagnostics only!!!
-c aaa=0.0D0
-c bbb=0.0D0
-c ael6i=0.0D0
-c ael3i=0.0D0
-C End diagnostics
ael6i=ael6(iteli,itelj)
ael3i=ael3(iteli,itelj)
dxj=dc(1,j)
dx_normj=dc_norm(1,j)
dy_normj=dc_norm(2,j)
dz_normj=dc_norm(3,j)
- xj=c(1,j)+0.5D0*dxj-xmedi
- yj=c(2,j)+0.5D0*dyj-ymedi
- zj=c(3,j)+0.5D0*dzj-zmedi
+C xj=c(1,j)+0.5D0*dxj-xmedi
+C yj=c(2,j)+0.5D0*dyj-ymedi
+C zj=c(3,j)+0.5D0*dzj-zmedi
+ xj=c(1,j)+0.5D0*dxj
+ yj=c(2,j)+0.5D0*dyj
+ zj=c(3,j)+0.5D0*dzj
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ isubchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ isubchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (isubchap.eq.1) then
+ xj=xj_temp-xmedi
+ yj=yj_temp-ymedi
+ zj=zj_temp-zmedi
+ else
+ xj=xj_safe-xmedi
+ yj=yj_safe-ymedi
+ zj=zj_safe-zmedi
+ endif
+C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC
+c 174 continue
+c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
+c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
+C Condition for being inside the proper box
+c if ((xj.gt.((0.5d0)*boxxsize)).or.
+c & (xj.lt.((-0.5d0)*boxxsize))) then
+c go to 174
+c endif
+c 175 continue
+c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
+c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
+C Condition for being inside the proper box
+c if ((yj.gt.((0.5d0)*boxysize)).or.
+c & (yj.lt.((-0.5d0)*boxysize))) then
+c go to 175
+c endif
+c 176 continue
+c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
+c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
+C Condition for being inside the proper box
+c if ((zj.gt.((0.5d0)*boxzsize)).or.
+c & (zj.lt.((-0.5d0)*boxzsize))) then
+c go to 176
+c endif
+C endif !endPBC condintion
+C xj=xj-xmedi
+C yj=yj-ymedi
+C zj=zj-zmedi
rij=xj*xj+yj*yj+zj*zj
+
+ sss=sscale(sqrt(rij))
+ sssgrad=sscagrad(sqrt(rij))
+c write (iout,*) "ij",i,j," rij",sqrt(rij)," r_cut",r_cut,
+c & " rlamb",rlamb," sss",sss
+c if (sss.gt.0.0d0) then
rrmij=1.0D0/rij
rij=dsqrt(rij)
rmij=1.0D0/rij
ev2=bbb*r6ij
fac3=ael6i*r6ij
fac4=ael3i*r3ij
- evdwij=ev1+ev2
+ evdwij=(ev1+ev2)
el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
el2=fac4*fac
- eesij=el1+el2
-c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij
+C MARYSIA
+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
- evdw1=evdw1+evdwij
+ 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,
cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
cd & xmedi,ymedi,zmedi,xj,yj,zj
+
+ if (energy_dec) then
+ write (iout,'(a6,2i5,0pf7.3,2i5,3e11.3)')
+ &'evdw1',i,j,evdwij
+ &,iteli,itelj,aaa,evdw1,sss
+ write (iout,'(a6,2i5,0pf7.3,2f8.3)') 'ees',i,j,eesij,
+ &fac_shield(i),fac_shield(j)
+ endif
+
C
C Calculate contributions to the Cartesian gradient.
C
#ifdef SPLITELE
- facvdw=-6*rrmij*(ev1+evdwij)
+ facvdw=-6*rrmij*(ev1+evdwij)*sss
facel=-3*rrmij*(el1+eesij)
fac1=fac
erij(1)=xj*rmij
erij(2)=yj*rmij
erij(3)=zj*rmij
- if (calc_grad) then
+
*
* Radial derivatives. First process both termini of the fragment (i,j)
-*
+*
+ if (calc_grad) then
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
- ghalf=0.5D0*ggg(k)
- gelc(k,i)=gelc(k,i)+ghalf
- gelc(k,j)=gelc(k,j)+ghalf
+ 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.
*
- do k=i+1,j-1
- do l=1,3
- gelc(l,k)=gelc(l,k)+ggg(l)
- enddo
- enddo
- ggg(1)=facvdw*xj
- ggg(2)=facvdw*yj
- ggg(3)=facvdw*zj
+cgrad do k=i+1,j-1
+cgrad do l=1,3
+cgrad gelc(l,k)=gelc(l,k)+ggg(l)
+cgrad enddo
+cgrad enddo
+ if (sss.gt.0.0) then
+ ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
+ else
+ ggg(1)=0.0
+ ggg(2)=0.0
+ ggg(3)=0.0
+ endif
+c do k=1,3
+c ghalf=0.5D0*ggg(k)
+c gvdwpp(k,i)=gvdwpp(k,i)+ghalf
+c gvdwpp(k,j)=gvdwpp(k,j)+ghalf
+c enddo
+c 9/28/08 AL Gradient compotents will be summed only at the end
do k=1,3
- ghalf=0.5D0*ggg(k)
- gvdwpp(k,i)=gvdwpp(k,i)+ghalf
- gvdwpp(k,j)=gvdwpp(k,j)+ghalf
+ gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
+ gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
enddo
*
* Loop over residues i+1 thru j-1.
*
- do k=i+1,j-1
- do l=1,3
- gvdwpp(l,k)=gvdwpp(l,k)+ggg(l)
- enddo
- enddo
+cgrad do k=i+1,j-1
+cgrad do l=1,3
+cgrad gvdwpp(l,k)=gvdwpp(l,k)+ggg(l)
+cgrad enddo
+cgrad enddo
+ endif ! calc_grad
#else
- facvdw=ev1+evdwij
- facel=el1+eesij
+C MARYSIA
+ facvdw=(ev1+evdwij)*sss
+ facel=(el1+eesij)
fac1=fac
fac=-3*rrmij*(facvdw+facvdw+facel)
erij(1)=xj*rmij
erij(2)=yj*rmij
erij(3)=zj*rmij
- if (calc_grad) then
*
* Radial derivatives. First process both termini of the fragment (i,j)
*
+ if (calc_grad) then
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
+c gelc(k,j)=gelc(k,j)+ghalf
+c enddo
+c 9/28/08 AL Gradient compotents will be summed only at the end
do k=1,3
- ghalf=0.5D0*ggg(k)
- gelc(k,i)=gelc(k,i)+ghalf
- gelc(k,j)=gelc(k,j)+ghalf
+ gelc_long(k,j)=gelc(k,j)+ggg(k)
+ gelc_long(k,i)=gelc(k,i)-ggg(k)
enddo
*
* Loop over residues i+1 thru j-1.
*
- do k=i+1,j-1
- do l=1,3
- gelc(l,k)=gelc(l,k)+ggg(l)
- enddo
+cgrad do k=i+1,j-1
+cgrad do l=1,3
+cgrad gelc(l,k)=gelc(l,k)+ggg(l)
+cgrad enddo
+cgrad enddo
+c 9/28/08 AL Gradient compotents will be summed only at the end
+ ggg(1)=facvdw*xj+sssgrad*rmij*evdwij*xj
+ ggg(2)=facvdw*yj+sssgrad*rmij*evdwij*yj
+ ggg(3)=facvdw*zj+sssgrad*rmij*evdwij*zj
+ do k=1,3
+ gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
+ gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
enddo
+ endif ! calc_grad
#endif
*
* Angular part
*
+ if (calc_grad) then
ecosa=2.0D0*fac3*fac1+fac4
fac4=-3.0D0*fac4
fac3=-6.0D0*fac3
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)
+c gelc(k,i)=gelc(k,i)+ghalf
+c & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
+c & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
+c gelc(k,j)=gelc(k,j)+ghalf
+c & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
+c & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
+c enddo
+cgrad do k=i+1,j-1
+cgrad do l=1,3
+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
- 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)
- 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)
+ 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))
+ & *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))
+ & *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
- do k=i+1,j-1
- do l=1,3
- gelc(l,k)=gelc(l,k)+ggg(l)
- enddo
- enddo
- endif
+C print *,"before33", gelc_long(1,i), gelc_long(1,j)
+C MARYSIA
+c endif !sscale
+ endif ! calc_grad
IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
& .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0
& .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms
C are computed for EVERY pair of non-contiguous peptide groups.
C
+
if (j.lt.nres-1) then
j1=j+1
j2=j-1
j2=j-2
endif
kkk=0
+ lll=0
do k=1,2
do l=1,2
kkk=kkk+1
muij(kkk)=mu(k,i)*mu(l,j)
+c write(iout,*) 'mumu=', mu(k,i),mu(l,j),i,j,k,l
+#ifdef NEWCORR
+ if (calc_grad) then
+ gmuij1(kkk)=gtb1(k,i+1)*mu(l,j)
+c write(iout,*) 'k=',k,i,gtb1(k,i+1),gtb1(k,i+1)*mu(l,j)
+ gmuij2(kkk)=gUb2(k,i)*mu(l,j)
+ gmuji1(kkk)=mu(k,i)*gtb1(l,j+1)
+c write(iout,*) 'l=',l,j,gtb1(l,j+1),gtb1(l,j+1)*mu(k,i)
+ gmuji2(kkk)=mu(k,i)*gUb2(l,j)
+ endif
+#endif
enddo
enddo
-cd write (iout,*) 'EELEC: i',i,' j',j
-cd write (iout,*) 'j',j,' j1',j1,' j2',j2
-cd write(iout,*) 'muij',muij
+#ifdef DEBUG
+ write (iout,*) 'EELEC: i',i,' j',j
+ write (iout,*) 'j',j,' j1',j1,' j2',j2
+ write(iout,*) 'muij',muij
+ write (iout,*) "uy",uy(:,i)
+ write (iout,*) "uz",uz(:,j)
+ write (iout,*) "erij",erij
+#endif
ury=scalar(uy(1,i),erij)
urz=scalar(uz(1,i),erij)
vry=scalar(uy(1,j),erij)
a23=scalar(uy(1,i),uz(1,j))-3*ury*vrz
a32=scalar(uz(1,i),uy(1,j))-3*urz*vry
a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz
-C For diagnostics only
-cd a22=1.0d0
-cd a23=1.0d0
-cd a32=1.0d0
-cd a33=1.0d0
fac=dsqrt(-ael6i)*r3ij
-cd write (2,*) 'fac=',fac
-C For diagnostics only
-cd fac=1.0d0
a22=a22*fac
a23=a23*fac
a32=a32*fac
cd write (iout,'(4i5,4f10.5)')
cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
-cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') (uy(k,i),k=1,3),
-cd & (uz(k,i),k=1,3),(uy(k,j),k=1,3),(uz(k,j),k=1,3)
+cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i),
+cd & uy(:,j),uz(:,j)
cd write (iout,'(4f10.5)')
cd & scalar(uy(1,i),uy(1,j)),scalar(uy(1,i),uz(1,j)),
cd & scalar(uz(1,i),uy(1,j)),scalar(uz(1,i),uz(1,j))
cd write (iout,'(4f10.5)') ury,urz,vry,vrz
-cd write (iout,'(2i3,9f10.5/)') i,j,
+cd write (iout,'(9f10.5/)')
cd & fac22,a22,fac23,a23,fac32,a32,fac33,a33,eel_loc_ij
- if (calc_grad) then
C Derivatives of the elements of A in virtual-bond vectors
+ if (calc_grad) then
call unormderiv(erij(1),unmat(1,1),rmij,erder(1,1))
-cd do k=1,3
-cd do l=1,3
-cd erder(k,l)=0.0d0
-cd enddo
-cd enddo
do k=1,3
uryg(k,1)=scalar(erder(1,k),uy(1,i))
uryg(k,2)=scalar(uygrad(1,k,1,i),erij(1))
vrzg(k,2)=scalar(uzgrad(1,k,1,j),erij(1))
vrzg(k,3)=scalar(uzgrad(1,k,2,j),erij(1))
enddo
-cd do k=1,3
-cd do l=1,3
-cd uryg(k,l)=0.0d0
-cd urzg(k,l)=0.0d0
-cd vryg(k,l)=0.0d0
-cd vrzg(k,l)=0.0d0
-cd enddo
-cd enddo
C Compute radial contributions to the gradient
facr=-3.0d0*rrmij
a22der=a22*facr
a23der=a23*facr
a32der=a32*facr
a33der=a33*facr
-cd a22der=0.0d0
-cd a23der=0.0d0
-cd a32der=0.0d0
-cd a33der=0.0d0
agg(1,1)=a22der*xj
agg(2,1)=a22der*yj
agg(3,1)=a22der*zj
enddo
do k=1,3
C Derivatives in DC(i)
- ghalf1=0.5d0*agg(k,1)
- ghalf2=0.5d0*agg(k,2)
- ghalf3=0.5d0*agg(k,3)
- ghalf4=0.5d0*agg(k,4)
+cgrad ghalf1=0.5d0*agg(k,1)
+cgrad ghalf2=0.5d0*agg(k,2)
+cgrad ghalf3=0.5d0*agg(k,3)
+cgrad ghalf4=0.5d0*agg(k,4)
aggi(k,1)=fac*(scalar(uygrad(1,k,1,i),uy(1,j))
- & -3.0d0*uryg(k,2)*vry)+ghalf1
+ & -3.0d0*uryg(k,2)*vry)!+ghalf1
aggi(k,2)=fac*(scalar(uygrad(1,k,1,i),uz(1,j))
- & -3.0d0*uryg(k,2)*vrz)+ghalf2
+ & -3.0d0*uryg(k,2)*vrz)!+ghalf2
aggi(k,3)=fac*(scalar(uzgrad(1,k,1,i),uy(1,j))
- & -3.0d0*urzg(k,2)*vry)+ghalf3
+ & -3.0d0*urzg(k,2)*vry)!+ghalf3
aggi(k,4)=fac*(scalar(uzgrad(1,k,1,i),uz(1,j))
- & -3.0d0*urzg(k,2)*vrz)+ghalf4
+ & -3.0d0*urzg(k,2)*vrz)!+ghalf4
C Derivatives in DC(i+1)
aggi1(k,1)=fac*(scalar(uygrad(1,k,2,i),uy(1,j))
- & -3.0d0*uryg(k,3)*vry)+agg(k,1)
+ & -3.0d0*uryg(k,3)*vry)!+agg(k,1)
aggi1(k,2)=fac*(scalar(uygrad(1,k,2,i),uz(1,j))
- & -3.0d0*uryg(k,3)*vrz)+agg(k,2)
+ & -3.0d0*uryg(k,3)*vrz)!+agg(k,2)
aggi1(k,3)=fac*(scalar(uzgrad(1,k,2,i),uy(1,j))
- & -3.0d0*urzg(k,3)*vry)+agg(k,3)
+ & -3.0d0*urzg(k,3)*vry)!+agg(k,3)
aggi1(k,4)=fac*(scalar(uzgrad(1,k,2,i),uz(1,j))
- & -3.0d0*urzg(k,3)*vrz)+agg(k,4)
+ & -3.0d0*urzg(k,3)*vrz)!+agg(k,4)
C Derivatives in DC(j)
aggj(k,1)=fac*(scalar(uygrad(1,k,1,j),uy(1,i))
- & -3.0d0*vryg(k,2)*ury)+ghalf1
+ & -3.0d0*vryg(k,2)*ury)!+ghalf1
aggj(k,2)=fac*(scalar(uzgrad(1,k,1,j),uy(1,i))
- & -3.0d0*vrzg(k,2)*ury)+ghalf2
+ & -3.0d0*vrzg(k,2)*ury)!+ghalf2
aggj(k,3)=fac*(scalar(uygrad(1,k,1,j),uz(1,i))
- & -3.0d0*vryg(k,2)*urz)+ghalf3
+ & -3.0d0*vryg(k,2)*urz)!+ghalf3
aggj(k,4)=fac*(scalar(uzgrad(1,k,1,j),uz(1,i))
- & -3.0d0*vrzg(k,2)*urz)+ghalf4
+ & -3.0d0*vrzg(k,2)*urz)!+ghalf4
C Derivatives in DC(j+1) or DC(nres-1)
aggj1(k,1)=fac*(scalar(uygrad(1,k,2,j),uy(1,i))
& -3.0d0*vryg(k,3)*ury)
& -3.0d0*vryg(k,3)*urz)
aggj1(k,4)=fac*(scalar(uzgrad(1,k,2,j),uz(1,i))
& -3.0d0*vrzg(k,3)*urz)
-cd aggi(k,1)=ghalf1
-cd aggi(k,2)=ghalf2
-cd aggi(k,3)=ghalf3
-cd aggi(k,4)=ghalf4
-C Derivatives in DC(i+1)
-cd aggi1(k,1)=agg(k,1)
-cd aggi1(k,2)=agg(k,2)
-cd aggi1(k,3)=agg(k,3)
-cd aggi1(k,4)=agg(k,4)
-C Derivatives in DC(j)
-cd aggj(k,1)=ghalf1
-cd aggj(k,2)=ghalf2
-cd aggj(k,3)=ghalf3
-cd aggj(k,4)=ghalf4
-C Derivatives in DC(j+1)
-cd aggj1(k,1)=0.0d0
-cd aggj1(k,2)=0.0d0
-cd aggj1(k,3)=0.0d0
-cd aggj1(k,4)=0.0d0
- if (j.eq.nres-1 .and. i.lt.j-2) then
- do l=1,4
- aggj1(k,l)=aggj1(k,l)+agg(k,l)
-cd aggj1(k,l)=agg(k,l)
- enddo
- endif
+cgrad if (j.eq.nres-1 .and. i.lt.j-2) then
+cgrad do l=1,4
+cgrad aggj1(k,l)=aggj1(k,l)+agg(k,l)
+cgrad enddo
+cgrad endif
enddo
- endif
-c goto 11111
-C Check the loc-el terms by numerical integration
+ endif ! calc_grad
acipa(1,1)=a22
acipa(1,2)=a23
acipa(2,1)=a32
acipa(2,2)=a33
a22=-a22
a23=-a23
+ if (calc_grad) then
do l=1,2
do k=1,3
agg(k,l)=-agg(k,l)
aggj1(k,l)=-aggj1(k,l)
enddo
enddo
+ endif ! calc_grad
if (j.lt.nres-1) then
a22=-a22
a32=-a32
enddo
endif
ENDIF ! WCORR
-11111 continue
IF (wel_loc.gt.0.0d0) THEN
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)
-cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
-cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
+#ifdef DEBUG
+ write (iout,*) "muij",muij," a22",a22," a23",a23," a32",a32,
+ & " a33",a33
+ write (iout,*) "ij",i,j," eel_loc_ij",eel_loc_ij,
+ & " wel_loc",wel_loc
+#endif
+ 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)
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+ & 'eelloc',i,j,eel_loc_ij
+c if (eel_loc_ij.ne.0)
+c & write (iout,'(a4,2i4,8f9.5)')'chuj',
+c & i,j,a22,muij(1),a23,muij(2),a32,muij(3),a33,muij(4)
+
eel_loc=eel_loc+eel_loc_ij
-C Partial derivatives in virtual-bond dihedral angles gamma
+C Now derivative over eel_loc
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)*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=',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)
+ & +a23*gmuij1(2)
+ & +a32*gmuij1(3)
+ & +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)
+ gloc(nphi+i,icg)=gloc(nphi+i,icg)+
+ & geel_loc_ij*wel_loc
+c write(iout,*) "derivative over thatai-1"
+c write(iout,*) a22*gmuij2(1), a23*gmuij2(2) ,a32*gmuij2(3),
+c & a33*gmuij2(4)
+ geel_loc_ij=
+ & a22*gmuij2(1)
+ & +a23*gmuij2(2)
+ & +a32*gmuij2(3)
+ & +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)
+ & +a32*gmuji1(3)
+ & +a33*gmuji1(4)
+c write(iout,*) "derivative over thataj"
+c write(iout,*) a22*gmuji1(1), a23*gmuji1(2) ,a32*gmuji1(3),
+c & a33*gmuji1(4)
+
+ 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)
+ & +a32*gmuji2(3)
+ & +a33*gmuji2(4)
+c write(iout,*) "derivative over thataj-1"
+c write(iout,*) a22*gmuji2(1), a23*gmuji2(2) ,a32*gmuji2(3),
+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)
- 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)
-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
-cd write(iout,*) 'aggi1',aggi1
-cd write(iout,*) 'aggj ',aggj
-cd write(iout,*) 'aggj1',aggj1
+ & (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))
+ & *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)
- enddo
- do k=i+2,j2
- do l=1,3
- gel_loc(l,k)=gel_loc(l,k)+ggg(l)
- enddo
+ 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)
+cgrad gel_loc(l,i)=gel_loc(l,i)+ghalf
+cgrad gel_loc(l,j)=gel_loc(l,j)+ghalf
enddo
+cgrad do k=i+1,j2
+cgrad do l=1,3
+cgrad gel_loc(l,k)=gel_loc(l,k)+ggg(l)
+cgrad enddo
+cgrad 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 ! calc_grad
ENDIF
- if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
-C Contributions from turns
- a_temp(1,1)=a22
- a_temp(1,2)=a23
- a_temp(2,1)=a32
- a_temp(2,2)=a33
- call eturn34(i,j,eello_turn3,eello_turn4)
- endif
+
+
C Change 12/26/95 to calculate four-body contributions to H-bonding energy
- if (j.gt.i+1 .and. num_conti.le.maxconts) then
+c if (j.gt.i+1 .and. num_conti.le.maxconts) then
+ if (wcorr+wcorr4+wcorr5+wcorr6.gt.0.0d0
+ & .and. num_conti.le.maxconts) then
+c write (iout,*) i,j," entered corr"
C
C Calculate the contact function. The ith column of the array JCONT will
C contain the numbers of atoms that make contacts with the atom I (of numbers
& ' will skip next contacts for this conf.'
else
jcont_hb(num_conti,i)=j
+cd write (iout,*) "i",i," j",j," num_conti",num_conti,
+cd & " jcont_hb",jcont_hb(num_conti,i)
IF (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.
& wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
C 9/30/99 (AL) - store components necessary to evaluate higher-order loc-el
a_chuj(2,1,num_conti,i)=a32
a_chuj(2,2,num_conti,i)=a33
C --- Gradient of rij
+ if (calc_grad) then
do kkk=1,3
grij_hb_cont(kkk,num_conti,i)=erij(kkk)
enddo
-c if (i.eq.1) then
-c a_chuj(1,1,num_conti,i)=-0.61d0
-c a_chuj(1,2,num_conti,i)= 0.4d0
-c a_chuj(2,1,num_conti,i)= 0.65d0
-c a_chuj(2,2,num_conti,i)= 0.50d0
-c else if (i.eq.2) then
-c a_chuj(1,1,num_conti,i)= 0.0d0
-c a_chuj(1,2,num_conti,i)= 0.0d0
-c a_chuj(2,1,num_conti,i)= 0.0d0
-c a_chuj(2,2,num_conti,i)= 0.0d0
-c endif
-C --- and its gradients
-cd write (iout,*) 'i',i,' j',j
-cd do kkk=1,3
-cd write (iout,*) 'iii 1 kkk',kkk
-cd write (iout,*) agg(kkk,:)
-cd enddo
-cd do kkk=1,3
-cd write (iout,*) 'iii 2 kkk',kkk
-cd write (iout,*) aggi(kkk,:)
-cd enddo
-cd do kkk=1,3
-cd write (iout,*) 'iii 3 kkk',kkk
-cd write (iout,*) aggi1(kkk,:)
-cd enddo
-cd do kkk=1,3
-cd write (iout,*) 'iii 4 kkk',kkk
-cd write (iout,*) aggj(kkk,:)
-cd enddo
-cd do kkk=1,3
-cd write (iout,*) 'iii 5 kkk',kkk
-cd write (iout,*) aggj1(kkk,:)
-cd enddo
kkll=0
do k=1,2
do l=1,2
a_chuj_der(k,l,m,3,num_conti,i)=aggi1(m,kkll)
a_chuj_der(k,l,m,4,num_conti,i)=aggj(m,kkll)
a_chuj_der(k,l,m,5,num_conti,i)=aggj1(m,kkll)
-c do mm=1,5
-c a_chuj_der(k,l,m,mm,num_conti,i)=0.0d0
-c enddo
enddo
enddo
enddo
+ endif ! calc_grad
ENDIF
IF (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) THEN
C Calculate contact energies
cosbg2=cosb-cosg
c fac3=dsqrt(-ael6i)/r0ij**3
fac3=dsqrt(-ael6i)*r3ij
- ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
- ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
+c ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
+ ees0tmp=4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1
+ if (ees0tmp.gt.0) then
+ ees0pij=dsqrt(ees0tmp)
+ else
+ ees0pij=0
+ endif
+c ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
+ ees0tmp=4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2
+ if (ees0tmp.gt.0) then
+ ees0mij=dsqrt(ees0tmp)
+ else
+ 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
c ees0m(num_conti,i)=0.0D0
C End diagnostics.
-c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij,
-c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont
- facont_hb(num_conti,i)=fcont
- if (calc_grad) then
+c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij,
+c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont
C Angular derivatives of the contact function
+
ees0pij1=fac3/ees0pij
ees0mij1=fac3/ees0mij
fac3p=-3.0D0*fac3*rrmij
c ecosbm=0.0D0
c ecosgm=0.0D0
C End diagnostics
+ facont_hb(num_conti,i)=fcont
+
+ if (calc_grad) then
fprimcont=fprimcont/rij
cd facont_hb(num_conti,i)=1.0D0
C Following line is for diagnostics.
gacont_hbr(2,num_conti,i)=fprimcont*yj
gacont_hbr(3,num_conti,i)=fprimcont*zj
do k=1,3
- ghalfp=0.5D0*gggp(k)
- ghalfm=0.5D0*gggm(k)
- gacontp_hb1(k,num_conti,i)=ghalfp
+c
+c 10/24/08 cgrad and ! comments indicate the parts of the code removed
+c following the change of gradient-summation algorithm.
+c
+cgrad ghalfp=0.5D0*gggp(k)
+cgrad ghalfm=0.5D0*gggm(k)
+ 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)
- gacontp_hb2(k,num_conti,i)=ghalfp
+ & *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)
- gacontm_hb1(k,num_conti,i)=ghalfm
+ & *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)
- gacontm_hb2(k,num_conti,i)=ghalfm
+ & *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!
cdiag do k=1,3
cdiag gacontp_hb1(k,num_conti,i)=0.0D0
cdiag gacontm_hb2(k,num_conti,i)=0.0D0
cdiag gacontm_hb3(k,num_conti,i)=0.0D0
cdiag enddo
+
+ endif ! calc_grad
+
ENDIF ! wcorr
endif ! num_conti.le.maxconts
endif ! fcont.gt.0
endif ! j.gt.i+1
- 1216 continue
- enddo ! j
- num_cont_hb(i)=num_conti
- 1215 continue
- enddo ! i
-cd do i=1,nres
-cd write (iout,'(i3,3f10.5,5x,3f10.5)')
-cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i)
-cd enddo
-c 12/7/99 Adam eello_turn3 will be considered as a separate energy term
-ccc eel_loc=eel_loc+eello_turn3
+ if (calc_grad) then
+ if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
+ do k=1,4
+ do l=1,3
+ ghalf=0.5d0*agg(l,k)
+ aggi(l,k)=aggi(l,k)+ghalf
+ aggi1(l,k)=aggi1(l,k)+agg(l,k)
+ aggj(l,k)=aggj(l,k)+ghalf
+ enddo
+ enddo
+ if (j.eq.nres-1 .and. i.lt.j-2) then
+ do k=1,4
+ do l=1,3
+ aggj1(l,k)=aggj1(l,k)+agg(l,k)
+ enddo
+ enddo
+ endif
+ endif
+ endif ! calc_grad
+c t_eelecij=t_eelecij+MPI_Wtime()-time00
return
end
C-----------------------------------------------------------------------------
- subroutine eturn34(i,j,eello_turn3,eello_turn4)
+ subroutine eturn3(i,eello_turn3)
C Third- and fourth-order contributions from turns
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.TORSION'
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),
- & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),gpizda1(2,2),
+ & gpizda2(2,2),auxgmat1(2,2),auxgmatt1(2,2),
+ & auxgmat2(2,2),auxgmatt2(2,2)
double precision agg(3,4),aggi(3,4),aggi1(3,4),
- & 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
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
+ & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
+ & num_conti,j1,j2
+ j=i+2
+c write (iout,*) "eturn3",i,j,j1,j2
+ a_temp(1,1)=a22
+ a_temp(1,2)=a23
+ a_temp(2,1)=a32
+ a_temp(2,2)=a33
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Third-order contributions
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd call checkint_turn3(i,a_temp,eello_turn3_num)
call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
+c auxalary matices for theta gradient
+c auxalary matrix for i+1 and constant i+2
+ call matmat2(gtEUg(1,1,i+1),EUg(1,1,i+2),auxgmat1(1,1))
+c auxalary matrix for i+2 and constant i+1
+ call matmat2(EUg(1,1,i+1),gtEUg(1,1,i+2),auxgmat2(1,1))
call transpose2(auxmat(1,1),auxmat1(1,1))
+ call transpose2(auxgmat1(1,1),auxgmatt1(1,1))
+ call transpose2(auxgmat2(1,1),auxgmatt2(1,1))
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)
+ if (energy_dec) write (iout,'(6heturn3,2i5,0pf7.3)') i,i+2,
+ & eello_t3
+ if (calc_grad) then
+C#ifdef NEWCORR
+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)
+C#endif
+
+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
- if (calc_grad) then
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))
+ 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),pizda(1,1))
- call matmat2(a_temp(1,1),pizda(1,1),pizda(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
- a_temp(1,1)=aggi(l,1)
- a_temp(1,2)=aggi(l,2)
- a_temp(2,1)=aggi(l,3)
- a_temp(2,2)=aggi(l,4)
+c ghalf1=0.5d0*agg(l,1)
+c ghalf2=0.5d0*agg(l,2)
+c ghalf3=0.5d0*agg(l,3)
+c ghalf4=0.5d0*agg(l,4)
+ a_temp(1,1)=aggi(l,1)!+ghalf1
+ a_temp(1,2)=aggi(l,2)!+ghalf2
+ a_temp(2,1)=aggi(l,3)!+ghalf3
+ a_temp(2,2)=aggi(l,4)!+ghalf4
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))
- a_temp(1,1)=aggi1(l,1)
- a_temp(1,2)=aggi1(l,2)
- a_temp(2,1)=aggi1(l,3)
- a_temp(2,2)=aggi1(l,4)
+ & *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)
+ a_temp(2,2)=aggi1(l,4)!+agg(l,4)
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))
- a_temp(1,1)=aggj(l,1)
- a_temp(1,2)=aggj(l,2)
- a_temp(2,1)=aggj(l,3)
- a_temp(2,2)=aggj(l,4)
+ & *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
+ a_temp(2,2)=aggj(l,4)!+ghalf4
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
- else if (j.eq.i+3 .and. itype(i+2).ne.21) then
+
+ endif ! calc_grad
+
+ return
+ end
+C-------------------------------------------------------------------------------
+ subroutine eturn4(i,eello_turn4)
+C Third- and fourth-order contributions from turns
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.CONTACTS'
+ include 'COMMON.TORSION'
+ 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),
+ & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2),auxgvec(2),
+ & auxgEvec1(2),auxgEvec2(2),auxgEvec3(2),
+ & gte1t(2,2),gte2t(2,2),gte3t(2,2),
+ & gte1a(2,2),gtae3(2,2),gtae3e2(2,2), ae3gte2(2,2),
+ & gtEpizda1(2,2),gtEpizda2(2,2),gtEpizda3(2,2)
+ double precision agg(3,4),aggi(3,4),aggi1(3,4),
+ & aggj(3,4),aggj1(3,4),a_temp(2,2),auxmat3(2,2)
+ common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33,
+ & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,
+ & num_conti,j1,j2
+ j=i+3
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd call checkint_turn4(i,a_temp,eello_turn4_num)
- iti1=itortyp(itype(i+1))
- iti2=itortyp(itype(i+2))
- iti3=itortyp(itype(i+3))
+c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
+c write(iout,*)"WCHODZE W PROGRAM"
+ a_temp(1,1)=a22
+ a_temp(1,2)=a23
+ a_temp(2,1)=a32
+ a_temp(2,2)=a33
+ iti1=itype2loc(itype(i+1))
+ iti2=itype2loc(itype(i+2))
+ iti3=itype2loc(itype(i+3))
+c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3
call transpose2(EUg(1,1,i+1),e1t(1,1))
call transpose2(Eug(1,1,i+2),e2t(1,1))
call transpose2(Eug(1,1,i+3),e3t(1,1))
+C Ematrix derivative in theta
+ call transpose2(gtEUg(1,1,i+1),gte1t(1,1))
+ call transpose2(gtEug(1,1,i+2),gte2t(1,1))
+ call transpose2(gtEug(1,1,i+3),gte3t(1,1))
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
+c eta1 in derivative theta
+ call matmat2(gte1t(1,1),a_temp(1,1),gte1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+c auxgvec is derivative of Ub2 so i+3 theta
+ call matvec2(e1a(1,1),gUb2(1,i+3),auxgvec(1))
+c auxalary matrix of E i+1
+ call matvec2(gte1a(1,1),Ub2(1,i+3),auxgEvec1(1))
+c s1=0.0
+c gs1=0.0
+ s1=scalar2(b1(1,i+2),auxvec(1))
+c derivative of theta i+2 with constant i+3
+ gs23=scalar2(gtb1(1,i+2),auxvec(1))
+c derivative of theta i+2 with constant i+2
+ gs32=scalar2(b1(1,i+2),auxgvec(1))
+c derivative of E matix in theta of i+1
+ gsE13=scalar2(b1(1,i+2),auxgEvec1(1))
+
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
+c ea31 in derivative theta
+ call matmat2(a_temp(1,1),gte3t(1,1),gtae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+c auxilary matrix auxgvec of Ub2 with constant E matirx
+ call matvec2(ae3(1,1),gUb2(1,i+2),auxgvec(1))
+c auxilary matrix auxgEvec1 of E matix with Ub2 constant
+ call matvec2(gtae3(1,1),Ub2(1,i+2),auxgEvec3(1))
+
+c s2=0.0
+c gs2=0.0
+ s2=scalar2(b1(1,i+1),auxvec(1))
+c derivative of theta i+1 with constant i+3
+ gs13=scalar2(gtb1(1,i+1),auxvec(1))
+c derivative of theta i+2 with constant i+1
+ gs21=scalar2(b1(1,i+1),auxgvec(1))
+c derivative of theta i+3 with constant i+1
+ gsE31=scalar2(b1(1,i+1),auxgEvec3(1))
+c write(iout,*) gs1,gs2,'i=',i,auxgvec(1),gUb2(1,i+2),gtb1(1,i+2),
+c & gtb1(1,i+1)
call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
+c two derivatives over diffetent matrices
+c gtae3e2 is derivative over i+3
+ call matmat2(gtae3(1,1),e2t(1,1),gtae3e2(1,1))
+c ae3gte2 is derivative over i+2
+ call matmat2(ae3(1,1),gte2t(1,1),ae3gte2(1,1))
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
+c three possible derivative over theta E matices
+c i+1
+ call matmat2(ae3e2(1,1),gte1t(1,1),gtEpizda1(1,1))
+c i+2
+ call matmat2(ae3gte2(1,1),e1t(1,1),gtEpizda2(1,1))
+c i+3
+ call matmat2(gtae3e2(1,1),e1t(1,1),gtEpizda3(1,1))
s3=0.5d0*(pizda(1,1)+pizda(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
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
+ & 'eturn4',i,j,-(s1+s2+s3)
+c write (iout,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
+c & ' eello_turn4_num',8*eello_turn4_num
C Derivatives in gamma(i)
- if (calc_grad) then
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))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),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))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1))
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))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
- call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1))
- call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
+ call matmat2(auxmat(1,1),e2t(1,1),auxmat3(1,1))
+ 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)
+ if (calc_grad) then
C Cartesian derivatives
C Derivatives of this turn contributions in DC(i+2)
if (j.lt.nres-1) then
a_temp(2,2)=agg(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
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))
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
a_temp(2,2)=aggi(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
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))
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)
a_temp(2,2)=aggi1(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
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))
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)
a_temp(2,2)=aggj(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
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))
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)
a_temp(2,2)=aggj1(l,4)
call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
- s1=scalar2(b1(1,iti2),auxvec(1))
+ s1=scalar2(b1(1,i+2),auxvec(1))
call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
- s2=scalar2(b1(1,iti1),auxvec(1))
+ s2=scalar2(b1(1,i+1),auxvec(1))
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))
+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
- endif
- endif
+
+ endif ! calc_grad
+
return
end
C-----------------------------------------------------------------------------
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'COMMON.LOCAL'
c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
c & ' scal14',scal14
do i=iatscp_s,iatscp_e
- if (itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
iteli=itel(i)
c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
-
+C Returning the ith atom to box
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
- if (itypj.eq.21) cycle
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
C Uncomment following three lines for SC-p interactions
c xj=c(1,nres+j)-xi
c yj=c(2,nres+j)-yi
c zj=c(3,nres+j)-zi
C Uncomment following three lines for Ca-p interactions
- xj=c(1,j)-xi
- yj=c(2,j)-yi
- zj=c(3,j)-zi
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+C returning the jth atom to box
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+C Finding the closest jth atom
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+C sss is scaling function for smoothing the cutoff gradient otherwise
+C the gradient would not be continuouse
+ sss=sscale(1.0d0/(dsqrt(rrij)))
+ if (sss.le.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/(dsqrt(rrij)))
fac=rrij**expon2
e1=fac*fac*aad(itypj,iteli)
e2=fac*bad(itypj,iteli)
if (iabs(j-i) .le. 2) then
e1=scal14*e1
e2=scal14*e2
- evdw2_14=evdw2_14+e1+e2
+ evdw2_14=evdw2_14+(e1+e2)*sss
endif
evdwij=e1+e2
-c write (iout,*) i,j,evdwij
- evdw2=evdw2+evdwij
+c write (iout,'(a6,2i5,0pf7.3,2i3,3e11.3)')
+c & 'evdw2',i,j,evdwij,iteli,itypj,fac,aad(itypj,iteli),
+c & bad(itypj,iteli)
+ evdw2=evdw2+evdwij*sss
if (calc_grad) then
C
C Calculate contributions to the gradient in the virtual-bond and SC vectors.
C
- fac=-(evdwij+e1)*rrij
+ fac=-(evdwij+e1)*rrij*sss
+ fac=fac+(evdwij)*sssgrad*dsqrt(rrij)/expon
ggg(1)=xj*fac
ggg(2)=yj*fac
ggg(3)=zj*fac
gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l)
enddo
enddo
- endif
+ endif ! calc_grad
enddo
enddo ! iint
1225 continue
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
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,*)'edis: nhpb=',nhpb,' fbr=',fbr
+c write(iout,*)'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. itype(iii).eq.1 .and. itype(jjj).eq.1) then
+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
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.VAR'
include 'COMMON.IOUNITS'
double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
- itypi=itype(i)
+ itypi=iabs(itype(i))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=dsc_inv(itypi)
- itypj=itype(j)
+ itypj=iabs(itype(j))
dscj_inv=dsc_inv(itypj)
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
c
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.LOCAL'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
include 'COMMON.CONTROL'
- logical energy_dec /.false./
double precision u(3),ud(3)
estr=0.0d0
+ estr1=0.0d0
+c write (iout,*) "distchainmax",distchainmax
do i=nnt+1,nct
- if (itype(i-1).eq.21 .or. itype(i).eq.21) then
- estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
- do j=1,3
- gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
- & *dc(j,i-1)/vbld(i)
- enddo
- if (energy_dec) write(iout,*)
- & "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax)
- else
+ if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle
+C estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax)
+C do j=1,3
+C gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax)
+C & *dc(j,i-1)/vbld(i)
+C enddo
+C if (energy_dec) write(iout,*)
+C & "estr1",i,vbld(i),distchainmax,
+C & gnmr1(vbld(i),-1.0d0,distchainmax)
+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
+ endif
estr=estr+diff*diff
do j=1,3
gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i)
enddo
- endif
-
+C endif
+C write (iout,'(a7,i5,4f7.3)')
+C & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff
enddo
- estr=0.5d0*AKP*estr
+ estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
c
do i=nnt,nct
- iti=itype(i)
- if (iti.ne.10 .and. iti.ne.21) then
+ iti=iabs(itype(i))
+ if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
diff=vbld(i+nres)-vbldsc0(1,iti)
-c write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
-c & AKSC(1,iti),AKSC(1,iti)*diff*diff
+C write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
+C & AKSC(1,iti),AKSC(1,iti)*diff*diff
estr=estr+0.5d0*AKSC(1,iti)*diff*diff
do j=1,3
gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
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.
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.LOCAL'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
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
c write (iout,*) ithet_start,ithet_end
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+C if (itype(i-1).eq.ntyp1) cycle
+ if (i.le.2) cycle
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
C Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
it=itype(i-1)
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ ichir1=isign(1,itype(i-2))
+ ichir2=isign(1,itype(i))
+ if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1))
+ if (itype(i).eq.10) ichir2=isign(1,itype(i-1))
+ if (itype(i-1).eq.10) then
+ itype1=isign(10,itype(i-2))
+ ichir11=isign(1,itype(i-2))
+ ichir12=isign(1,itype(i-2))
+ itype2=isign(10,itype(i))
+ ichir21=isign(1,itype(i))
+ ichir22=isign(1,itype(i))
+ endif
+ if (i.eq.3) then
+ y(1)=0.0D0
+ y(2)=0.0D0
+ else
+
+ 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)
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ endif
+ 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)
C In following comments this theta will be referred to as t_c.
thet_pred_mean=0.0d0
do k=1,2
- athetk=athet(k,it)
- bthetk=bthet(k,it)
+ athetk=athet(k,it,ichir1,ichir2)
+ bthetk=bthet(k,it,ichir1,ichir2)
+ if (it.eq.10) then
+ athetk=athet(k,itype1,ichir11,ichir12)
+ bthetk=bthet(k,itype2,ichir21,ichir22)
+ endif
thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
enddo
c write (iout,*) "thet_pred_mean",thet_pred_mean
thet_pred_mean=thet_pred_mean*ss+a0thet(it)
c write (iout,*) "thet_pred_mean",thet_pred_mean
C Derivatives of the "mean" values in gamma1 and gamma2.
- dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
- dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
+ dthetg1=(-athet(1,it,ichir1,ichir2)*y(2)
+ &+athet(2,it,ichir1,ichir2)*y(1))*ss
+ dthetg2=(-bthet(1,it,ichir1,ichir2)*z(2)
+ & +bthet(2,it,ichir1,ichir2)*z(1))*ss
+ if (it.eq.10) then
+ dthetg1=(-athet(1,itype1,ichir11,ichir12)*y(2)
+ &+athet(2,itype1,ichir11,ichir12)*y(1))*ss
+ dthetg2=(-bthet(1,itype2,ichir21,ichir22)*z(2)
+ & +bthet(2,itype2,ichir21,ichir22)*z(1))*ss
+ endif
if (theta(i).gt.pi-delta) then
call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
& E_tc0)
& E_theta,E_tc)
endif
etheta=etheta+ethetai
+c write (iout,'(a6,i5,0pf7.3,f7.3,i5)')
+c & 'ebend',i,ethetai,theta(i),itype(i)
c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i),
c & rad2deg*phii,rad2deg*phii1,ethetai
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
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.LOCAL'
include 'COMMON.GEO'
include 'COMMON.INTERACT'
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),
etheta=0.0D0
c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
do i=ithet_start,ithet_end
- if (itype(i-1).eq.21) cycle
+C if (i.eq.2) cycle
+C if (itype(i-1).eq.ntyp1) cycle
+ if (i.le.2) cycle
+ if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
+ & .or.itype(i).eq.ntyp1) cycle
+ if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1)).ne.20) iblock=1
dethetai=0.0d0
dephii=0.0d0
dephii1=0.0d0
theti2=0.5d0*theta(i)
- ityp2=ithetyp(itype(i-1))
+ ityp2=ithetyp((itype(i-1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(i-2).ne.21) then
+ if (i.eq.3) then
+ phii=0.0d0
+ ityp1=nthetyp+1
+ do k=1,nsingle
+ cosph1(k)=0.0d0
+ sinph1(k)=0.0d0
+ enddo
+ else
+ if (i.gt.3 .and. itype(i-3).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
#else
phii=phi(i)
#endif
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp((itype(i-2)))
do k=1,nsingle
cosph1(k)=dcos(k*phii)
sinph1(k)=dsin(k*phii)
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
endif
- if (i.lt.nres .and. itype(i).ne.21) then
+ endif
+ if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
#else
phii1=phi(i+1)
#endif
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp((itype(i)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
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
c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
c call flush(iout)
- ethetai=aa0thet(ityp1,ityp2,ityp3)
+ ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
do k=1,ndouble
do l=1,k-1
ccl=cosph1(l)*cosph2(k-l)
enddo
endif
do k=1,ntheterm
- ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
- dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+ ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
& *coskt(k)
if (lprn)
- & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+ & write (iout,*) "k",k,"
+ & aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
& " ethetai",ethetai
enddo
if (lprn) then
endif
do m=1,ntheterm2
do k=1,nsingle
- aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
- & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
- & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
- & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+ & +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+ & +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+ & +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*aux*coskt(m)
dephii=dephii+k*sinkt(m)*(
- & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
- & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ & ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
dephii1=dephii1+k*sinkt(m)*(
- & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
- & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ & eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+ & ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
if (lprn)
& write (iout,*) "m",m," k",k," bbthet",
- & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
- & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
- & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
- & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+ & 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
enddo
enddo
if (lprn)
do m=1,ntheterm3
do k=2,ndouble
do l=1,k-1
- aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
ethetai=ethetai+sinkt(m)*aux
dethetai=dethetai+0.5d0*m*coskt(m)*aux
dephii=dephii+l*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
dephii1=dephii1+(k-l)*sinkt(m)*(
- & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
- & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
- & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
- & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
if (lprn) then
write (iout,*) "m",m," k",k," l",l," ffthet",
- & ffthet(l,k,m,ityp1,ityp2,ityp3),
- & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
- & ggthet(l,k,m,ityp1,ityp2,ityp3),
- & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ & ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+ & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+ & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+ & " ethetai",ethetai
write (iout,*) cosph1ph2(l,k)*sinkt(m),
& cosph1ph2(k,l)*sinkt(m),
& sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
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
return
end
C ALPHA and OMEGA.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
common /sccalc/ time11,time12,time112,theti,it,nlobit
delta=0.02d0*pi
escloc=0.0D0
-c write (iout,'(a)') 'ESC'
+C write (iout,*) 'ESC'
do i=loc_start,loc_end
it=itype(i)
- if (it.eq.21) cycle
+ if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
- nlobit=nlob(it)
+ nlobit=nlob(iabs(it))
c print *,'i=',i,' it=',it,' nlobit=',nlobit
-c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
+C write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
theti=theta(i+1)-pipol
x(1)=dtan(theti)
x(2)=alph(i)
dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
enddo
dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
-c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
-c & esclocbi,ss,ssd
+ write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
+ & esclocbi,ss,ssd
escloci=ss*escloci+(1.0d0-ss)*esclocbi
c escloci=esclocbi
c write (iout,*) escloci
enddo
dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
-c & esclocbi,ss,ssd
+c & esclocbi,ss,ssd
escloci=ss*escloci+(1.0d0-ss)*esclocbi
-c write (iout,*) escloci
+C write (iout,*) 'i=',i, escloci
else
call enesc(x,escloci,dersc,ddummy,.false.)
endif
escloc=escloc+escloci
-c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
+C write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
+ write (iout,'(a6,i5,0pf7.3)')
+ & 'escloc',i,escloci
gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
& wscloc*dersc(1)
do iii=-1,1
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j,iii)+emin)
cd print *,'j=',j,' expfac=',expfac
escloc_i=escloc_i+expfac
do k=1,3
dersc12=0.0d0
do j=1,nlobit
- expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
+ expfac=dexp(bsc(j,iabs(it))-0.5D0*contr(j)+emin)
escloc_i=escloc_i+expfac
do k=1,2
dersc(k)=dersc(k)+Ax(k,j)*expfac
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
include 'COMMON.VAR'
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.21) cycle
+ if (itype(i).eq.ntyp1) cycle
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
cosfac=dsqrt(cosfac2)
sinfac2=0.5d0/(1.0d0-costtab(i+1))
sinfac=dsqrt(sinfac2)
- it=itype(i)
+ it=iabs(itype(i))
if (it.eq.10) goto 1
c
C Compute the axes of tghe local cartesian coordinates system; store in
y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
enddo
do j = 1,3
- z_prime(j) = -uz(j,i-1)
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
enddo
c write (2,*) "i",i
c write (2,*) "x_prime",(x_prime(j),j=1,3)
C Compute the energy of the ith side cbain
C
c write (2,*) "xx",xx," yy",yy," zz",zz
- it=itype(i)
+ it=iabs(itype(i))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
Cc diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0d0,itype(i))*dsin(alph(2))*dsin(omeg(2))
write(2,'(3f8.1,3f9.3,1x,3f9.3)')
& alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
& xx1,yy1,zz1
c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
c write (2,*) "escloc",escloc
+c write (2,*) "i",i," escloc",sumene,escloc,it,itype(i),
+c & zz,xx,yy
if (.not. calc_grad) goto 1
#ifdef DEBUG
C
dZZ_Ci1(k)=0.0d0
dZZ_Ci(k)=0.0d0
do j=1,3
- dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
- dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+ dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+ & *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
subroutine splinthet(theti,delta,ss,ssder)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.VAR'
include 'COMMON.GEO'
thetup=pi-delta
C-----------------------------------------------------------------------------
#ifdef CRYST_TOR
C-----------------------------------------------------------------------------
- subroutine etor(etors,edihcnstr,fact)
+ subroutine etor(etors,fact)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+ & .or. itype(i).eq.ntyp1) cycle
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
enddo
-! 6/20/98 - dihedral angle constraints
- edihcnstr=0.0d0
- do i=1,ndih_constr
- itori=idih_constr(i)
- phii=phi(itori)
- 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
- 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
- endif
-! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
-! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
- enddo
-! write (iout,*) 'edihcnstr',edihcnstr
return
end
c------------------------------------------------------------------------------
#else
- subroutine etor(etors,edihcnstr,fact)
+ subroutine etor(etors,fact)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
c lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21) cycle
+ if (i.le.2) 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
+C if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+C & .or. itype(i).eq.ntyp1) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
+ if (iabs(itype(i)).eq.20) then
+ iblock=2
+ else
+ iblock=1
+ endif
itori=itortyp(itype(i-2))
itori1=itortyp(itype(i-1))
phii=phi(i)
gloci=0.0D0
C Regular cosine and sine terms
- do j=1,nterm(itori,itori1)
- v1ij=v1(j,itori,itori1)
- v2ij=v2(j,itori,itori1)
+ do j=1,nterm(itori,itori1,iblock)
+ v1ij=v1(j,itori,itori1,iblock)
+ v2ij=v2(j,itori,itori1,iblock)
cosphi=dcos(j*phii)
sinphi=dsin(j*phii)
etors=etors+v1ij*cosphi+v2ij*sinphi
C
cosphi=dcos(0.5d0*phii)
sinphi=dsin(0.5d0*phii)
- do j=1,nlor(itori,itori1)
+ do j=1,nlor(itori,itori1,iblock)
vl1ij=vlor1(j,itori,itori1)
vl2ij=vlor2(j,itori,itori1)
vl3ij=vlor3(j,itori,itori1)
pom=vl2ij*cosphi+vl3ij*sinphi
pom1=1.0d0/(pom*pom+1.0d0)
etors=etors+vl1ij*pom1
+c if (energy_dec) etors_ii=etors_ii+
+c & vl1ij*pom1
pom=-pom*pom1*pom1
gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
enddo
C Subtract the constant term
- etors=etors-v0(itori,itori1)
+ etors=etors-v0(itori,itori1,iblock)
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
+ & (v1(j,itori,itori1,1),j=1,6),(v2(j,itori,itori1,1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
1215 continue
enddo
-! 6/20/98 - dihedral angle constraints
- edihcnstr=0.0d0
- do i=1,ndih_constr
- itori=idih_constr(i)
- phii=phi(itori)
- difi=pinorm(phii-phi0(i))
- 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
- 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
- else
- difi=0.0d0
- endif
-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)
- enddo
-! write (iout,*) 'edihcnstr',edihcnstr
return
end
c----------------------------------------------------------------------------
C 6/23/01 Compute double torsional energy
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
c lprn=.true.
etors_d=0.0D0
do i=iphi_start,iphi_end-1
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21
- & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle
+ if (i.le.3) cycle
+C if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1
+C & .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if ((itype(i-2).eq.ntyp1).or.itype(i-3).eq.ntyp1.or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i).eq.ntyp1).or.
+ & (itype(i+1).eq.ntyp1)) cycle
if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
& goto 1215
itori=itortyp(itype(i-2))
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
+ iblock=1
+ if (iabs(itype(i+1)).eq.20) iblock=2
C Regular cosine and sine terms
- do j=1,ntermd_1(itori,itori1,itori2)
- v1cij=v1c(1,j,itori,itori1,itori2)
- v1sij=v1s(1,j,itori,itori1,itori2)
- v2cij=v1c(2,j,itori,itori1,itori2)
- v2sij=v1s(2,j,itori,itori1,itori2)
+ do j=1,ntermd_1(itori,itori1,itori2,iblock)
+ v1cij=v1c(1,j,itori,itori1,itori2,iblock)
+ v1sij=v1s(1,j,itori,itori1,itori2,iblock)
+ v2cij=v1c(2,j,itori,itori1,itori2,iblock)
+ v2sij=v1s(2,j,itori,itori1,itori2,iblock)
cosphi1=dcos(j*phii)
sinphi1=dsin(j*phii)
cosphi2=dcos(j*phii1)
gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
enddo
- do k=2,ntermd_2(itori,itori1,itori2)
+ do k=2,ntermd_2(itori,itori1,itori2,iblock)
do l=1,k-1
- v1cdij = v2c(k,l,itori,itori1,itori2)
- v2cdij = v2c(l,k,itori,itori1,itori2)
- v1sdij = v2s(k,l,itori,itori1,itori2)
- v2sdij = v2s(l,k,itori,itori1,itori2)
+ v1cdij = v2c(k,l,itori,itori1,itori2,iblock)
+ v2cdij = v2c(l,k,itori,itori1,itori2,iblock)
+ v1sdij = v2s(k,l,itori,itori1,itori2,iblock)
+ v2sdij = v2s(l,k,itori,itori1,itori2,iblock)
cosphi1p2=dcos(l*phii+(k-l)*phii1)
cosphi1m2=dcos(l*phii-(k-l)*phii1)
sinphi1p2=dsin(l*phii+(k-l)*phii1)
gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
& -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
- & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
+ & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
enddo
enddo
gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
return
end
#endif
+c---------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine etor_kcc(etors,fact)
+ 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'
+ double precision c1(0:maxval_kcc),c2(0:maxval_kcc)
+ logical lprn
+c double precision thybt1(maxtermkcc),thybt2(maxtermkcc)
+C Set lprn=.true. for debugging
+ lprn=energy_dec
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode
+ 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(itype(i-2))
+ itori1=itortyp(itype(i-1))
+ phii=phi(i)
+ glocig=0.0D0
+ glocit1=0.0d0
+ glocit2=0.0d0
+C to avoid multiple devision by 2
+c theti22=0.5d0*theta(i)
+C theta 12 is the theta_1 /2
+C theta 22 is theta_2 /2
+c theti12=0.5d0*theta(i-1)
+C and appropriate sinus function
+ sinthet1=dsin(theta(i-1))
+ sinthet2=dsin(theta(i))
+ costhet1=dcos(theta(i-1))
+ costhet2=dcos(theta(i))
+C to speed up lets store its mutliplication
+ sint1t2=sinthet2*sinthet1
+ sint1t2n=1.0d0
+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
+ nval=nterm_kcc_Tb(itori,itori1)
+ c1(0)=0.0d0
+ c2(0)=0.0d0
+ c1(1)=1.0d0
+ c2(1)=1.0d0
+ do j=2,nval
+ c1(j)=c1(j-1)*costhet1
+ c2(j)=c2(j-1)*costhet2
+ enddo
+ etori=0.0d0
+ do j=1,nterm_kcc(itori,itori1)
+ cosphi=dcos(j*phii)
+ sinphi=dsin(j*phii)
+ sint1t2n1=sint1t2n
+ sint1t2n=sint1t2n*sint1t2
+ sumvalc=0.0d0
+ gradvalct1=0.0d0
+ gradvalct2=0.0d0
+ do k=1,nval
+ do l=1,nval
+ sumvalc=sumvalc+v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
+ gradvalct1=gradvalct1+
+ & (k-1)*v1_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
+ gradvalct2=gradvalct2+
+ & (l-1)*v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
+ enddo
+ enddo
+ gradvalct1=-gradvalct1*sinthet1
+ gradvalct2=-gradvalct2*sinthet2
+ sumvals=0.0d0
+ gradvalst1=0.0d0
+ gradvalst2=0.0d0
+ do k=1,nval
+ do l=1,nval
+ sumvals=sumvals+v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
+ gradvalst1=gradvalst1+
+ & (k-1)*v2_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
+ gradvalst2=gradvalst2+
+ & (l-1)*v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
+ enddo
+ enddo
+ gradvalst1=-gradvalst1*sinthet1
+ gradvalst2=-gradvalst2*sinthet2
+ etori=etori+sint1t2n*(sumvalc*cosphi+sumvals*sinphi)
+C glocig is the gradient local i site in gamma
+ glocig=glocig+j*sint1t2n*(sumvals*cosphi-sumvalc*sinphi)
+C now gradient over theta_1
+ glocit1=glocit1+sint1t2n*(gradvalct1*cosphi+gradvalst1*sinphi)
+ & +j*sint1t2n1*costhet1*sinthet2*(sumvalc*cosphi+sumvals*sinphi)
+ glocit2=glocit2+sint1t2n*(gradvalct2*cosphi+gradvalst2*sinphi)
+ & +j*sint1t2n1*sinthet1*costhet2*(sumvalc*cosphi+sumvals*sinphi)
+ enddo ! j
+ etors=etors+etori
+C derivative over gamma
+ gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig
+C derivative over theta1
+ gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1
+C now derivative over theta2
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2
+ if (lprn)
+ & write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1,
+ & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori
+ enddo
+ return
+ end
+c---------------------------------------------------------------------------------------------
+ subroutine etor_constr(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'
+! 6/20/98 - dihedral angle constraints
+ edihcnstr=0.0d0
+c do i=1,ndih_constr
+c write (iout,*) "idihconstr_start",idihconstr_start,
+c & " idihconstr_end",idihconstr_end
+ if (raw_psipred) then
+ do i=idihconstr_start,idihconstr_end
+ itori=idih_constr(i)
+ phii=phi(itori)
+ gaudih_i=vpsipred(1,i)
+ gauder_i=0.0d0
+ do j=1,2
+ s = sdihed(j,i)
+ cos_i=(1.0d0-dcos(phii-phibound(j,i)))/s**2
+ dexpcos_i=dexp(-cos_i*cos_i)
+ gaudih_i=gaudih_i+vpsipred(j+1,i)*dexpcos_i
+ gauder_i=gauder_i-2*vpsipred(j+1,i)*dsin(phii-phibound(j,i))
+ & *cos_i*dexpcos_i/s**2
+ enddo
+ edihcnstr=edihcnstr-wdihc*dlog(gaudih_i)
+ gloc(itori-3,icg)=gloc(itori-3,icg)-wdihc*gauder_i/gaudih_i
+ if (energy_dec)
+ & write (iout,'(2i5,f8.3,f8.5,2(f8.5,2f8.3),f10.5)')
+ & i,itori,phii*rad2deg,vpsipred(1,i),vpsipred(2,i),
+ & phibound(1,i)*rad2deg,sdihed(1,i)*rad2deg,vpsipred(3,i),
+ & phibound(2,i)*rad2deg,sdihed(2,i)*rad2deg,
+ & -wdihc*dlog(gaudih_i)
+ enddo
+ else
+ 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----------------------------------------------------------------------------
+C The rigorous attempt to derive energy function
+ subroutine ebend_kcc(etheta)
+
+ 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(maxang_kcc)
+C Set lprn=.true. for debugging
+ lprn=energy_dec
+c lprn=.true.
+C print *,"wchodze kcc"
+ if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode
+ etheta=0.0D0
+ do i=ithet_start,ithet_end
+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
+ iti=iabs(itortyp(itype(i-1)))
+ sinthet=dsin(theta(i))
+ costhet=dcos(theta(i))
+ do j=1,nbend_kcc_Tb(iti)
+ thybt1(j)=v1bend_chyb(j,iti)
+ enddo
+ sumth1thyb=v1bend_chyb(0,iti)+
+ & tschebyshev(1,nbend_kcc_Tb(iti),thybt1(1),costhet)
+ if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg,
+ & sumth1thyb
+ ihelp=nbend_kcc_Tb(iti)-1
+ gradthybt1=gradtschebyshev(0,ihelp,thybt1(1),costhet)
+ etheta=etheta+sumth1thyb
+C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0)
+ gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)-wang*gradthybt1*sinthet
+ enddo
+ return
+ end
+c-------------------------------------------------------------------------------------
+ subroutine etheta_constr(ethetacnstr)
+
+ 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'
+ 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
+c------------------------------------------------------------------------------
c------------------------------------------------------------------------------
subroutine eback_sc_corr(esccor)
c 7/21/2007 Correlations between the backbone-local and side-chain-local
c amino-acid residues.
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.VAR'
include 'COMMON.GEO'
include 'COMMON.LOCAL'
c lprn=.true.
c write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
esccor=0.0D0
- do i=iphi_start,iphi_end
- if (itype(i-2).eq.21 .or. itype(i-1).eq.21) cycle
+ do i=itau_start,itau_end
+ if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- itori=itype(i-2)
- itori1=itype(i-1)
+ isccori=isccortyp(itype(i-2))
+ isccori1=isccortyp(itype(i-1))
phii=phi(i)
+ do intertyp=1,3 !intertyp
+cc Added 09 May 2012 (Adasko)
+cc Intertyp means interaction type of backbone mainchain correlation:
+c 1 = SC...Ca...Ca...Ca
+c 2 = Ca...Ca...Ca...SC
+c 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- do j=1,nterm_sccor
- v1ij=v1sccor(j,itori,itori1)
- v2ij=v2sccor(j,itori,itori1)
- cosphi=dcos(j*phii)
- sinphi=dsin(j*phii)
- esccor=esccor+v1ij*cosphi+v2ij*sinphi
- gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
- enddo
+ if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
+ & (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-1).eq.ntyp1)))
+ & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
+ & .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+ & .or.(itype(i).eq.ntyp1)))
+ & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
+ & (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+ & (itype(i-3).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
+ & cycle
+ do j=1,nterm_sccor(isccori,isccori1)
+ v1ij=v1sccor(j,intertyp,isccori,isccori1)
+ v2ij=v2sccor(j,intertyp,isccori,isccori1)
+ cosphi=dcos(j*tauangle(intertyp,i))
+ sinphi=dsin(j*tauangle(intertyp,i))
+ 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
if (lprn)
& write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
& restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
- & (v1sccor(j,itori,itori1),j=1,6),(v2sccor(j,itori,itori1),j=1,6)
- gsccor_loc(i-3)=gloci
+ & (v1sccor(j,1,itori,itori1),j=1,6)
+ & ,(v2sccor(j,1,itori,itori1),j=1,6)
+c gsccor_loc(i-3)=gloci
+ enddo !intertyp
enddo
return
end
return
end
c------------------------------------------------------------------------------
-#ifdef MPL
- subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- integer dimen1,dimen2,atom,indx
- double precision buffer(dimen1,dimen2)
- double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
- num_kont=num_cont_hb(atom)
- do i=1,num_kont
- do k=1,7
- do j=1,3
- buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k)
- enddo ! j
- enddo ! k
- buffer(i,indx+22)=facont_hb(i,atom)
- buffer(i,indx+23)=ees0p(i,atom)
- buffer(i,indx+24)=ees0m(i,atom)
- buffer(i,indx+25)=dfloat(jcont_hb(i,atom))
- enddo ! i
- buffer(1,indx+26)=dfloat(num_kont)
- return
- end
-c------------------------------------------------------------------------------
- subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- integer dimen1,dimen2,atom,indx
- double precision buffer(dimen1,dimen2)
- double precision zapas
- common /contacts_hb/ zapas(3,20,maxres,7),
- & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
- & num_cont_hb(maxres),jcont_hb(20,maxres)
- num_kont=buffer(1,indx+26)
- num_kont_old=num_cont_hb(atom)
- num_cont_hb(atom)=num_kont+num_kont_old
- do i=1,num_kont
- ii=i+num_kont_old
- do k=1,7
- do j=1,3
- zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
- enddo ! j
- enddo ! k
- facont_hb(ii,atom)=buffer(i,indx+22)
- ees0p(ii,atom)=buffer(i,indx+23)
- ees0m(ii,atom)=buffer(i,indx+24)
- jcont_hb(ii,atom)=buffer(i,indx+25)
- enddo ! i
- return
- end
-c------------------------------------------------------------------------------
-#endif
subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
C This subroutine calculates multi-body contributions to hydrogen-bonding
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
-#ifdef MPL
- include 'COMMON.INFO'
-#endif
include 'COMMON.FFIELD'
include 'COMMON.DERIV'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
-#ifdef MPL
- parameter (max_cont=maxconts)
- parameter (max_dim=2*(8*3+2))
- parameter (msglen1=max_cont*max_dim*4)
- parameter (msglen2=2*msglen1)
- integer source,CorrelType,CorrelID,Error
- double precision buffer(max_cont,max_dim)
-#endif
double precision gx(3),gx1(3)
logical lprn,ldone
C Set lprn=.true. for debugging
lprn=.false.
-#ifdef MPL
- n_corr=0
- n_corr1=0
- if (fgProcs.le.1) goto 30
- if (lprn) then
- write (iout,'(a)') 'Contact function values:'
- do i=nnt,nct-2
- write (iout,'(2i3,50(1x,i2,f5.2))')
- & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
- & j=1,num_cont_hb(i))
- enddo
- endif
-C Caution! Following code assumes that electrostatic interactions concerning
-C a given atom are split among at most two processors!
- CorrelType=477
- CorrelID=MyID+1
- ldone=.false.
- do i=1,max_cont
- do j=1,max_dim
- buffer(i,j)=0.0D0
- enddo
- enddo
- mm=mod(MyRank,2)
-cd write (iout,*) 'MyRank',MyRank,' mm',mm
- if (mm) 20,20,10
- 10 continue
-cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
- if (MyRank.gt.0) then
-C Send correlation contributions to the preceding processor
- msglen=msglen1
- nn=num_cont_hb(iatel_s)
- call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
-cd write (iout,*) 'The BUFFER array:'
-cd do i=1,nn
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
-cd enddo
- if (ielstart(iatel_s).gt.iatel_s+ispp) then
- msglen=msglen2
- call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
-C Clear the contacts of the atom passed to the neighboring processor
- nn=num_cont_hb(iatel_s+1)
-cd do i=1,nn
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
-cd enddo
- num_cont_hb(iatel_s)=0
- endif
-cd write (iout,*) 'Processor ',MyID,MyRank,
-cd & ' is sending correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen
-cd write (*,*) 'Processor ',MyID,MyRank,
-cd & ' is sending correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
- call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
-cd write (iout,*) 'Processor ',MyID,
-cd & ' has sent correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelID=',CorrelID
-cd write (*,*) 'Processor ',MyID,
-cd & ' has sent correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelID=',CorrelID
- msglen=msglen1
- endif ! (MyRank.gt.0)
- if (ldone) goto 30
- ldone=.true.
- 20 continue
-cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
- if (MyRank.lt.fgProcs-1) then
-C Receive correlation contributions from the next processor
- msglen=msglen1
- if (ielend(iatel_e).lt.nct-1) msglen=msglen2
-cd write (iout,*) 'Processor',MyID,
-cd & ' is receiving correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
-cd write (*,*) 'Processor',MyID,
-cd & ' is receiving correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
- nbytes=-1
- do while (nbytes.le.0)
- call mp_probe(MyID+1,CorrelType,nbytes)
- enddo
-cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
- call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
-cd write (iout,*) 'Processor',MyID,
-cd & ' has received correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' nbytes=',nbytes
-cd write (iout,*) 'The received BUFFER array:'
-cd do i=1,max_cont
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
-cd enddo
- if (msglen.eq.msglen1) then
- call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
- else if (msglen.eq.msglen2) then
- call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
- call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
- else
- write (iout,*)
- & 'ERROR!!!! message length changed while processing correlations.'
- write (*,*)
- & 'ERROR!!!! message length changed while processing correlations.'
- call mp_stopall(Error)
- endif ! msglen.eq.msglen1
- endif ! MyRank.lt.fgProcs-1
- if (ldone) goto 30
- ldone=.true.
- goto 10
- 30 continue
-#endif
if (lprn) then
write (iout,'(a)') 'Contact function values:'
do i=nnt,nct-2
C This subroutine calculates multi-body contributions to hydrogen-bonding
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
-#ifdef MPL
- include 'COMMON.INFO'
+#ifdef MPI
+ include "mpif.h"
#endif
include 'COMMON.FFIELD'
include 'COMMON.DERIV'
+ include 'COMMON.LOCAL'
include 'COMMON.INTERACT'
include 'COMMON.CONTACTS'
-#ifdef MPL
- parameter (max_cont=maxconts)
- parameter (max_dim=2*(8*3+2))
- parameter (msglen1=max_cont*max_dim*4)
- parameter (msglen2=2*msglen1)
- integer source,CorrelType,CorrelID,Error
- double precision buffer(max_cont,max_dim)
-#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SHIELD'
double precision gx(3),gx1(3)
+ integer num_cont_hb_old(maxres)
logical lprn,ldone
-
+ double precision eello4,eello5,eelo6,eello_turn6
+ external eello4,eello5,eello6,eello_turn6
C Set lprn=.true. for debugging
lprn=.false.
eturn6=0.0d0
-#ifdef MPL
- n_corr=0
- n_corr1=0
- if (fgProcs.le.1) goto 30
- if (lprn) then
- write (iout,'(a)') 'Contact function values:'
- do i=nnt,nct-2
- write (iout,'(2i3,50(1x,i2,f5.2))')
- & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
- & j=1,num_cont_hb(i))
- enddo
- endif
-C Caution! Following code assumes that electrostatic interactions concerning
-C a given atom are split among at most two processors!
- CorrelType=477
- CorrelID=MyID+1
- ldone=.false.
- do i=1,max_cont
- do j=1,max_dim
- buffer(i,j)=0.0D0
- enddo
- enddo
- mm=mod(MyRank,2)
-cd write (iout,*) 'MyRank',MyRank,' mm',mm
- if (mm) 20,20,10
- 10 continue
-cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
- if (MyRank.gt.0) then
-C Send correlation contributions to the preceding processor
- msglen=msglen1
- nn=num_cont_hb(iatel_s)
- call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
-cd write (iout,*) 'The BUFFER array:'
-cd do i=1,nn
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
-cd enddo
- if (ielstart(iatel_s).gt.iatel_s+ispp) then
- msglen=msglen2
- call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
-C Clear the contacts of the atom passed to the neighboring processor
- nn=num_cont_hb(iatel_s+1)
-cd do i=1,nn
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
-cd enddo
- num_cont_hb(iatel_s)=0
- endif
-cd write (iout,*) 'Processor ',MyID,MyRank,
-cd & ' is sending correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen
-cd write (*,*) 'Processor ',MyID,MyRank,
-cd & ' is sending correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
- call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
-cd write (iout,*) 'Processor ',MyID,
-cd & ' has sent correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelID=',CorrelID
-cd write (*,*) 'Processor ',MyID,
-cd & ' has sent correlation contribution to processor',MyID-1,
-cd & ' msglen=',msglen,' CorrelID=',CorrelID
- msglen=msglen1
- endif ! (MyRank.gt.0)
- if (ldone) goto 30
- ldone=.true.
- 20 continue
-cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
- if (MyRank.lt.fgProcs-1) then
-C Receive correlation contributions from the next processor
- msglen=msglen1
- if (ielend(iatel_e).lt.nct-1) msglen=msglen2
-cd write (iout,*) 'Processor',MyID,
-cd & ' is receiving correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
-cd write (*,*) 'Processor',MyID,
-cd & ' is receiving correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' CorrelType=',CorrelType
- nbytes=-1
- do while (nbytes.le.0)
- call mp_probe(MyID+1,CorrelType,nbytes)
- enddo
-cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
- call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
-cd write (iout,*) 'Processor',MyID,
-cd & ' has received correlation contribution from processor',MyID+1,
-cd & ' msglen=',msglen,' nbytes=',nbytes
-cd write (iout,*) 'The received BUFFER array:'
-cd do i=1,max_cont
-cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
-cd enddo
- if (msglen.eq.msglen1) then
- call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
- else if (msglen.eq.msglen2) then
- call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
- call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
- else
- write (iout,*)
- & 'ERROR!!!! message length changed while processing correlations.'
- write (*,*)
- & 'ERROR!!!! message length changed while processing correlations.'
- call mp_stopall(Error)
- endif ! msglen.eq.msglen1
- endif ! MyRank.lt.fgProcs-1
- if (ldone) goto 30
- ldone=.true.
- goto 10
- 30 continue
-#endif
if (lprn) then
write (iout,'(a)') 'Contact function values:'
do i=nnt,nct-2
- write (iout,'(2i3,50(1x,i2,f5.2))')
- & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
- & j=1,num_cont_hb(i))
+ write (iout,'(2i3,50(1x,i2,5f6.3))')
+ & i,num_cont_hb(i),(jcont_hb(j,i),d_cont(j,i),
+ & ((a_chuj(ll,kk,j,i),ll=1,2),kk=1,2),j=1,num_cont_hb(i))
enddo
endif
ecorr=0.0D0
num_conti=num_cont_hb(i)
do jj=1,num_conti
j=jcont_hb(jj,i)
+#ifdef MOMENT
call dipole(i,j,jj)
+#endif
enddo
enddo
endif
C Calculate the local-electrostatic correlation terms
- do i=iatel_s,iatel_e+1
+c write (iout,*) "gradcorr5 in eello5 before loop"
+c do iii=1,nres
+c write (iout,'(i5,3f10.5)')
+c & iii,(gradcorr5(jjj,iii),jjj=1,3)
+c enddo
+ do i=min0(iatel_s,iturn4_start),max0(iatel_e+1,iturn3_end+1)
+c write (iout,*) "corr loop i",i
i1=i+1
num_conti=num_cont_hb(i)
num_conti1=num_cont_hb(i+1)
do jj=1,num_conti
j=jcont_hb(jj,i)
+ jp=iabs(j)
do kk=1,num_conti1
j1=jcont_hb(kk,i1)
-c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
+ jp1=iabs(j1)
+c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
c & ' jj=',jj,' kk=',kk
- if (j1.eq.j+1 .or. j1.eq.j-1) then
+c if (j1.eq.j+1 .or. j1.eq.j-1) then
+ if ((j.gt.0 .and. j1.gt.0 .or. j.gt.0 .and. j1.lt.0
+ & .or. j.lt.0 .and. j1.gt.0) .and.
+ & (jp1.eq.jp+1 .or. jp1.eq.jp-1)) then
C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
C The system gains extra energy.
n_corr=n_corr+1
IF (sred_geom.lt.cutoff_corr) THEN
call gcont(sred_geom,r0_corr,1.0D0,delt_corr,
& ekont,fprimcont)
-c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
-c & ' jj=',jj,' kk=',kk
+cd write (iout,*) 'i=',i,' j=',jp,' i1=',i1,' j1=',jp1,
+cd & ' jj=',jj,' kk=',kk
fac_prim1=0.5d0*sqd2/sqd1*fprimcont
fac_prim2=0.5d0*sqd1/sqd2*fprimcont
do l=1,3
enddo
n_corr1=n_corr1+1
cd write (iout,*) 'sred_geom=',sred_geom,
-cd & ' ekont=',ekont,' fprim=',fprimcont
- call calc_eello(i,j,i+1,j1,jj,kk)
+cd & ' ekont=',ekont,' fprim=',fprimcont,
+cd & ' fac_prim1',fac_prim1,' fac_prim2',fac_prim2
+cd write (iout,*) "g_contij",g_contij
+cd write (iout,*) "grij_hb_cont i",grij_hb_cont(:,jj,i)
+cd write (iout,*) "grij_hb_cont i1",grij_hb_cont(:,jj,i1)
+ call calc_eello(i,jp,i+1,jp1,jj,kk)
if (wcorr4.gt.0.0d0)
- & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk)
+ & 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)
+c write (iout,*) "gradcorr5 before eello5"
+c do iii=1,nres
+c write (iout,'(i5,3f10.5)')
+c & iii,(gradcorr5(jjj,iii),jjj=1,3)
+c enddo
if (wcorr5.gt.0.0d0)
- & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk)
-c print *,"wcorr5",ecorr5
+ & ecorr5=ecorr5+eello5(i,jp,i+1,jp1,jj,kk)
+c write (iout,*) "gradcorr5 after eello5"
+c do iii=1,nres
+c write (iout,'(i5,3f10.5)')
+c & iii,(gradcorr5(jjj,iii),jjj=1,3)
+c enddo
+ if (energy_dec.and.wcorr5.gt.0.0d0)
+ 1 write (iout,'(a6,4i5,0pf7.3)')
+ 2 'ecorr5',i,j,i+1,j1,eello5(i,jp,i+1,jp1,jj,kk)
cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6
-cd write(2,*)'ijkl',i,j,i+1,j1
- if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
+cd write(2,*)'ijkl',i,jp,i+1,jp1
+ if (wcorr6.gt.0.0d0 .and. (jp.ne.i+4 .or. jp1.ne.i+3
& .or. wturn6.eq.0.0d0))then
cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
- ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
+ ecorr6=ecorr6+eello6(i,jp,i+1,jp1,jj,kk)
+ if (energy_dec) write (iout,'(a6,4i5,0pf7.3)')
+ 1 'ecorr6',i,j,i+1,j1,eello6(i,jp,i+1,jp1,jj,kk)
cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
cd & 'ecorr6=',ecorr6
cd write (iout,'(4e15.5)') sred_geom,
-cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
-cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
-cd & dabs(eello6(i,j,i+1,j1,jj,kk))
+cd & dabs(eello4(i,jp,i+1,jp1,jj,kk)),
+cd & dabs(eello5(i,jp,i+1,jp1,jj,kk)),
+cd & dabs(eello6(i,jp,i+1,jp1,jj,kk))
else if (wturn6.gt.0.0d0
- & .and. (j.eq.i+4 .and. j1.eq.i+3)) then
-cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
+ & .and. (jp.eq.i+4 .and. jp1.eq.i+3)) then
+cd write (iout,*) '******eturn6: i,j,i+1,j1',i,jip,i+1,jp1
eturn6=eturn6+eello_turn6(i,jj,kk)
+ if (energy_dec) write (iout,'(a6,4i5,0pf7.3)')
+ 1 'eturn6',i,j,i+1,j1,eello_turn6(i,jj,kk)
cd write (2,*) 'multibody_eello:eturn6',eturn6
endif
ENDIF
-1111 continue
- else if (j1.eq.j) then
-C Contacts I-J and I-(J+1) occur simultaneously.
-C The system loses extra energy.
-c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
+1111 continue
endif
enddo ! kk
- do kk=1,num_conti
- j1=jcont_hb(kk,i)
-c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
-c & ' jj=',jj,' kk=',kk
- if (j1.eq.j+1) then
-C Contacts I-J and (I+1)-J occur simultaneously.
-C The system loses extra energy.
-c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
- endif ! j1==j+1
- enddo ! kk
enddo ! jj
enddo ! i
+ do i=1,nres
+ num_cont_hb(i)=num_cont_hb_old(i)
+ enddo
+c write (iout,*) "gradcorr5 in eello5"
+c do iii=1,nres
+c write (iout,'(i5,3f10.5)')
+c & iii,(gradcorr5(jjj,iii),jjj=1,3)
+c enddo
return
end
c------------------------------------------------------------------------------
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
cd ees0pij=1.0D0
cd ees0mkl=0.0D0
cd ees0mij=1.0D0
-c write (iout,*)'Contacts have occurred for peptide groups',i,j,
-c & ' and',k,l
-c write (iout,*)'Contacts have occurred for peptide groups',
-c & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
-c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
+c write (iout,'(2(a,2i3,a,f10.5,a,2f10.5),a,f10.5,a,$)')
+c & 'Contacts ',i,j,
+c & ' eij',eij,' eesij',ees0pij,ees0mij,' and ',k,l
+c & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' energy=',ekont*ees,
+c & 'gradcorr_long'
C Calculate the multi-body contribution to energy.
- ecorr=ecorr+ekont*ees
- if (calc_grad) then
+C ecorr=ecorr+ekont*ees
C Calculate multi-body contributions to the gradient.
+ coeffpees0pij=coeffp*ees0pij
+ coeffmees0mij=coeffm*ees0mij
+ coeffpees0pkl=coeffp*ees0pkl
+ coeffmees0mkl=coeffm*ees0mkl
do ll=1,3
- ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i)
- gradcorr(ll,i)=gradcorr(ll,i)+ghalf
- & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+
- & coeffm*ees0mkl*gacontm_hb1(ll,jj,i))
- gradcorr(ll,j)=gradcorr(ll,j)+ghalf
- & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+
- & coeffm*ees0mkl*gacontm_hb2(ll,jj,i))
- ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k)
- gradcorr(ll,k)=gradcorr(ll,k)+ghalf
- & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+
- & coeffm*ees0mij*gacontm_hb1(ll,kk,k))
- gradcorr(ll,l)=gradcorr(ll,l)+ghalf
- & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+
- & coeffm*ees0mij*gacontm_hb2(ll,kk,k))
- enddo
- do m=i+1,j-1
- do ll=1,3
- gradcorr(ll,m)=gradcorr(ll,m)+
- & ees*ekl*gacont_hbr(ll,jj,i)-
- & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
- & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
- enddo
+cgrad ghalfi=ees*ekl*gacont_hbr(ll,jj,i)
+ gradcorr(ll,i)=gradcorr(ll,i)!+0.5d0*ghalfi
+ & -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+
+ & coeffmees0mkl*gacontm_hb1(ll,jj,i))
+ gradcorr(ll,j)=gradcorr(ll,j)!+0.5d0*ghalfi
+ & -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+
+ & coeffmees0mkl*gacontm_hb2(ll,jj,i))
+cgrad ghalfk=ees*eij*gacont_hbr(ll,kk,k)
+ gradcorr(ll,k)=gradcorr(ll,k)!+0.5d0*ghalfk
+ & -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+
+ & coeffmees0mij*gacontm_hb1(ll,kk,k))
+ gradcorr(ll,l)=gradcorr(ll,l)!+0.5d0*ghalfk
+ & -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+
+ & coeffmees0mij*gacontm_hb2(ll,kk,k))
+ gradlongij=ees*ekl*gacont_hbr(ll,jj,i)-
+ & ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+
+ & coeffmees0mkl*gacontm_hb3(ll,jj,i))
+ gradcorr_long(ll,j)=gradcorr_long(ll,j)+gradlongij
+ gradcorr_long(ll,i)=gradcorr_long(ll,i)-gradlongij
+ gradlongkl=ees*eij*gacont_hbr(ll,kk,k)-
+ & ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+
+ & coeffmees0mij*gacontm_hb3(ll,kk,k))
+ gradcorr_long(ll,l)=gradcorr_long(ll,l)+gradlongkl
+ gradcorr_long(ll,k)=gradcorr_long(ll,k)-gradlongkl
+c write (iout,'(2f10.5,2x,$)') gradlongij,gradlongkl
enddo
- do m=k+1,l-1
- do ll=1,3
- gradcorr(ll,m)=gradcorr(ll,m)+
- & ees*eij*gacont_hbr(ll,kk,k)-
- & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
- & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
- enddo
- enddo
- endif
+c write (iout,*)
+cgrad do m=i+1,j-1
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+
+cgrad & ees*ekl*gacont_hbr(ll,jj,i)-
+cgrad & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
+cgrad & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
+cgrad enddo
+cgrad enddo
+cgrad do m=k+1,l-1
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+
+cgrad & ees*eij*gacont_hbr(ll,kk,k)-
+cgrad & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
+cgrad & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
+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
C---------------------------------------------------------------------------
subroutine dipole(i,j,jj)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.FFIELD'
& auxmat(2,2)
iti1 = itortyp(itype(i+1))
if (j.lt.nres-1) then
- itj1 = itortyp(itype(j+1))
+ itj1 = itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
do iii=1,2
dipi(iii,1)=Ub2(iii,i)
dipderi(iii)=Ub2der(iii,i)
- dipi(iii,2)=b1(iii,iti1)
+ dipi(iii,2)=b1(iii,i+1)
dipj(iii,1)=Ub2(iii,j)
dipderj(iii)=Ub2der(iii,j)
- dipj(iii,2)=b1(iii,itj1)
+ dipj(iii,2)=b1(iii,j+1)
enddo
kkk=0
do iii=1,2
dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
enddo
enddo
- if (.not.calc_grad) return
do kkk=1,5
do lll=1,3
mmm=0
enddo
return
end
+#endif
C---------------------------------------------------------------------------
subroutine calc_eello(i,j,k,l,jj,kk)
C
C
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l,
cd & ' jj=',jj,' kk=',kk
cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return
+cd write (iout,*) "a_chujij",((a_chuj(iii,jjj,jj,i),iii=1,2),jjj=1,2)
+cd write (iout,*) "a_chujkl",((a_chuj(iii,jjj,kk,k),iii=1,2),jjj=1,2)
do iii=1,2
do jjj=1,2
aa1(iii,jjj)=a_chuj(iii,jjj,jj,i)
if (l.eq.j+1) then
C parallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itj=itype2loc(itype(j))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
C A1 kernel(j+1) A2T
cd do iii=1,2
C indluded.
IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
call transpose2(AEA(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
call transpose2(AEAderg(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
- call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
- call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1))
call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
call transpose2(AEA(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
call transpose2(AEAderg(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j),AEAb1derg(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
- call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
- call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),b1(1,l+1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,l+1),AEAb1derg(1,2,2))
call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
do kkk=1,5
do lll=1,3
call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),
+ call matvec2(auxmat(1,1),b1(1,i),
& AEAb1derx(1,lll,kkk,iii,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),
& AEAb2derx(1,lll,kkk,iii,1,1))
- call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& AEAb1derx(1,lll,kkk,iii,2,1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
& AEAb2derx(1,lll,kkk,iii,2,1))
call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj),
+ call matvec2(auxmat(1,1),b1(1,j),
& AEAb1derx(1,lll,kkk,iii,1,2))
call matvec2(auxmat(1,1),Ub2(1,j),
& AEAb2derx(1,lll,kkk,iii,1,2))
- call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,l+1),
& AEAb1derx(1,lll,kkk,iii,2,2))
call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
& AEAb2derx(1,lll,kkk,iii,2,2))
else
C Antiparallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itype2loc(itype(i))
else
- iti=ntortyp+1
+ iti=nloctyp
endif
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
C A2 kernel(j-1)T A1T
call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
& (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
call transpose2(AEA(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
call transpose2(AEAderg(1,1,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
+ call matvec2(auxmat(1,1),b1(1,i),AEAb1derg(1,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
- call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
- call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
+ call matvec2(AEA(1,1,1),b1(1,k+1),AEAb1(1,2,1))
+ call matvec2(AEAderg(1,1,1),b1(1,k+1),AEAb1derg(1,2,1))
call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
call transpose2(AEA(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,j+1),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
call transpose2(AEAderg(1,1,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
+ call matvec2(auxmat(1,1),b1(1,l),AEAb1(1,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
- call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
- call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
+ call matvec2(AEA(1,1,2),b1(1,j+1),AEAb1(1,2,2))
+ call matvec2(AEAderg(1,1,2),b1(1,j+1),AEAb1derg(1,2,2))
call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
do kkk=1,5
do lll=1,3
call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,iti),
+ call matvec2(auxmat(1,1),b1(1,i),
& AEAb1derx(1,lll,kkk,iii,1,1))
call matvec2(auxmat(1,1),Ub2(1,i),
& AEAb2derx(1,lll,kkk,iii,1,1))
- call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& AEAb1derx(1,lll,kkk,iii,2,1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
& AEAb2derx(1,lll,kkk,iii,2,1))
call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
- call matvec2(auxmat(1,1),b1(1,itl),
+ call matvec2(auxmat(1,1),b1(1,l),
& AEAb1derx(1,lll,kkk,iii,1,2))
call matvec2(auxmat(1,1),Ub2(1,l),
& AEAb2derx(1,lll,kkk,iii,1,2))
- call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
+ call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,j+1),
& AEAb1derx(1,lll,kkk,iii,2,2))
call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
& AEAb2derx(1,lll,kkk,iii,2,2))
double precision function eello4(i,j,k,l,jj,kk)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
l2=l-2
endif
do ll=1,3
-cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i)
- ggg1(ll)=eel4*g_contij(ll,1)
- ggg2(ll)=eel4*g_contij(ll,2)
- ghalf=0.5d0*ggg1(ll)
-cd ghalf=0.0d0
- gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1)
+cgrad ggg1(ll)=eel4*g_contij(ll,1)
+cgrad ggg2(ll)=eel4*g_contij(ll,2)
+ glongij=eel4*g_contij(ll,1)+ekont*derx(ll,1,1)
+ glongkl=eel4*g_contij(ll,2)+ekont*derx(ll,1,2)
+cgrad ghalf=0.5d0*ggg1(ll)
+ gradcorr(ll,i)=gradcorr(ll,i)+ekont*derx(ll,2,1)
gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1)
- gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr(ll,j)=gradcorr(ll,j)+ekont*derx(ll,4,1)
gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1)
-cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k)
- ghalf=0.5d0*ggg2(ll)
-cd ghalf=0.0d0
- gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr_long(ll,j)=gradcorr_long(ll,j)+glongij
+ gradcorr_long(ll,i)=gradcorr_long(ll,i)-glongij
+cgrad ghalf=0.5d0*ggg2(ll)
+ gradcorr(ll,k)=gradcorr(ll,k)+ekont*derx(ll,2,2)
gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2)
- gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr(ll,l)=gradcorr(ll,l)+ekont*derx(ll,4,2)
gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2)
+ gradcorr_long(ll,l)=gradcorr_long(ll,l)+glongkl
+ gradcorr_long(ll,k)=gradcorr_long(ll,k)-glongkl
enddo
-cd goto 1112
- do m=i+1,j-1
- do ll=1,3
-cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i)
- gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
- enddo
- enddo
- do m=k+1,l-1
- do ll=1,3
-cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k)
- gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
- enddo
- enddo
-1112 continue
- do m=i+2,j2
- do ll=1,3
- gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
- enddo
- enddo
- do m=k+2,l2
- do ll=1,3
- gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
- enddo
- enddo
+cgrad do m=i+1,j-1
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+1,l-1
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
+cgrad enddo
+cgrad enddo
+cgrad do m=i+2,j2
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+2,l2
+cgrad do ll=1,3
+cgrad gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
+cgrad enddo
+cgrad enddo
cd do iii=1,nres-3
cd write (2,*) iii,gcorr_loc(iii)
cd enddo
- endif
+ endif ! calc_grad
eello4=ekont*eel4
cd write (2,*) 'ekont',ekont
cd write (iout,*) 'eello4',ekont*eel4
double precision function eello5(i,j,k,l,jj,kk)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
cd write (iout,*)
cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
cd & ' and',k,l
- itk=itortyp(itype(k))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk=itype2loc(itype(k))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
eello5_1=0.0d0
eello5_2=0.0d0
eello5_3=0.0d0
vv(2)=pizda(1,2)+pizda(2,1)
eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k))
& +0.5d0*scalar2(vv(1),Dtobr2(1,i))
- if (calc_grad) then
+ if (calc_grad) then
C Explicit gradient in virtual-dihedral angles.
if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1)
& +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k))
enddo
enddo
enddo
+ endif ! calc_grad
c goto 1112
- endif
c1111 continue
C Contribution from graph II
- call transpose2(EE(1,1,itk),auxmat(1,1))
+ call transpose2(EE(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
- eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
+ eello5_2=scalar2(AEAb1(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k))
if (calc_grad) then
C Explicit gradient in virtual-dihedral angles.
vv(2)=pizda(2,1)-pizda(1,2)
if (l.eq.j+1) then
g_corr5_loc(l-1)=g_corr5_loc(l-1)
- & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k)))
else
g_corr5_loc(j-1)=g_corr5_loc(j-1)
- & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
+ & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k)))
endif
C Cartesian gradient
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,iii)=derx(lll,kkk,iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,k))
& -0.5d0*scalar2(vv(1),Ctobr(1,k))
enddo
enddo
enddo
+ endif ! calc_grad
cd goto 1112
- endif
cd1111 continue
if (l.eq.j+1) then
cd goto 1110
enddo
enddo
cd goto 1112
- endif
C Contribution from graph IV
cd1110 continue
- call transpose2(EE(1,1,itl),auxmat(1,1))
+ call transpose2(EE(1,1,l),auxmat(1,1))
call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
- eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l))
- if (calc_grad) then
C Explicit gradient in virtual-dihedral angles.
g_corr5_loc(l-1)=g_corr5_loc(l-1)
& -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
g_corr5_loc(k-1)=g_corr5_loc(k-1)
- & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l)))
C Cartesian gradient
do iii=1,2
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,iii)=derx(lll,kkk,iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,l))
& -0.5d0*scalar2(vv(1),Ctobr(1,l))
enddo
enddo
enddo
- endif
+ endif ! calc_grad
else
C Antiparallel orientation
C Contribution from graph III
enddo
enddo
enddo
+ endif ! calc_grad
cd goto 1112
- endif
C Contribution from graph IV
1110 continue
- call transpose2(EE(1,1,itj),auxmat(1,1))
+ call transpose2(EE(1,1,j),auxmat(1,1))
call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
- eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
+ eello5_4=scalar2(AEAb1(1,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j))
if (calc_grad) then
C Explicit gradient in virtual-dihedral angles.
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
g_corr5_loc(k-1)=g_corr5_loc(k-1)
- & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
+ & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j)))
C Cartesian gradient
do iii=1,2
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
- & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
+ & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,j))
& -0.5d0*scalar2(vv(1),Ctobr(1,j))
enddo
enddo
enddo
- endif
+ endif ! calc_grad
endif
1112 continue
eel5=eello5_1+eello5_2+eello5_3+eello5_4
cd ekl=1.0d0
cd ekont=1.0d0
cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont
+C 2/11/08 AL Gradients over DC's connecting interacting sites will be
+C summed up outside the subrouine as for the other subroutines
+C handling long-range interactions. The old code is commented out
+C with "cgrad" to keep track of changes.
do ll=1,3
- ggg1(ll)=eel5*g_contij(ll,1)
- ggg2(ll)=eel5*g_contij(ll,2)
+cgrad ggg1(ll)=eel5*g_contij(ll,1)
+cgrad ggg2(ll)=eel5*g_contij(ll,2)
+ gradcorr5ij=eel5*g_contij(ll,1)+ekont*derx(ll,1,1)
+ gradcorr5kl=eel5*g_contij(ll,2)+ekont*derx(ll,1,2)
+c write (iout,'(a,3i3,a,5f8.3,2i3,a,5f8.3,a,f8.3)')
+c & "ecorr5",ll,i,j," derx",derx(ll,2,1),derx(ll,3,1),derx(ll,4,1),
+c & derx(ll,5,1),k,l," derx",derx(ll,2,2),derx(ll,3,2),
+c & derx(ll,4,2),derx(ll,5,2)," ekont",ekont
+c write (iout,'(a,3i3,a,3f8.3,2i3,a,3f8.3)')
+c & "ecorr5",ll,i,j," gradcorr5",g_contij(ll,1),derx(ll,1,1),
+c & gradcorr5ij,
+c & k,l," gradcorr5",g_contij(ll,2),derx(ll,1,2),gradcorr5kl
cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i)
- ghalf=0.5d0*ggg1(ll)
+cgrad ghalf=0.5d0*ggg1(ll)
cd ghalf=0.0d0
- gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr5(ll,i)=gradcorr5(ll,i)+ekont*derx(ll,2,1)
gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1)
- gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr5(ll,j)=gradcorr5(ll,j)+ekont*derx(ll,4,1)
gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1)
+ gradcorr5_long(ll,j)=gradcorr5_long(ll,j)+gradcorr5ij
+ gradcorr5_long(ll,i)=gradcorr5_long(ll,i)-gradcorr5ij
cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
- ghalf=0.5d0*ggg2(ll)
+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
+ endif ! calc_grad
cd goto 1112
- do m=i+1,j-1
- do ll=1,3
+cgrad do m=i+1,j-1
+cgrad do ll=1,3
cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i)
- gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
- enddo
- enddo
- do m=k+1,l-1
- do ll=1,3
+cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+1,l-1
+cgrad do ll=1,3
cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k)
- gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
- enddo
- enddo
+cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
+cgrad enddo
+cgrad enddo
c1112 continue
- do m=i+2,j2
- do ll=1,3
- gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
- enddo
- enddo
- do m=k+2,l2
- do ll=1,3
- gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
- enddo
- enddo
+cgrad do m=i+2,j2
+cgrad do ll=1,3
+cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+2,l2
+cgrad do ll=1,3
+cgrad gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
+cgrad enddo
+cgrad enddo
cd do iii=1,nres-3
cd write (2,*) iii,g_corr5_loc(iii)
cd enddo
- endif
eello5=ekont*eel5
cd write (2,*) 'ekont',ekont
cd write (iout,*) 'eello5',ekont*eel5
double precision function eello6(i,j,k,l,jj,kk)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
endif
C If turn contributions are considered, they will be handled separately.
eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6
-cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num
-cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num
-cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num
-cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num
-cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num
-cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num
+cd write(iout,*) 'eello6_1',eello6_1!,' eel6_1_num',16*eel6_1_num
+cd write(iout,*) 'eello6_2',eello6_2!,' eel6_2_num',16*eel6_2_num
+cd write(iout,*) 'eello6_3',eello6_3!,' eel6_3_num',16*eel6_3_num
+cd write(iout,*) 'eello6_4',eello6_4!,' eel6_4_num',16*eel6_4_num
+cd write(iout,*) 'eello6_5',eello6_5!,' eel6_5_num',16*eel6_5_num
+cd write(iout,*) 'eello6_6',eello6_6!,' eel6_6_num',16*eel6_6_num
cd goto 1112
if (calc_grad) then
if (j.lt.nres-1) then
l2=l-2
endif
do ll=1,3
- ggg1(ll)=eel6*g_contij(ll,1)
- ggg2(ll)=eel6*g_contij(ll,2)
+cgrad ggg1(ll)=eel6*g_contij(ll,1)
+cgrad ggg2(ll)=eel6*g_contij(ll,2)
cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i)
- ghalf=0.5d0*ggg1(ll)
+cgrad ghalf=0.5d0*ggg1(ll)
cd ghalf=0.0d0
- gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1)
+ gradcorr6ij=eel6*g_contij(ll,1)+ekont*derx(ll,1,1)
+ gradcorr6kl=eel6*g_contij(ll,2)+ekont*derx(ll,1,2)
+ gradcorr6(ll,i)=gradcorr6(ll,i)+ekont*derx(ll,2,1)
gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1)
- gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1)
+ gradcorr6(ll,j)=gradcorr6(ll,j)+ekont*derx(ll,4,1)
gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1)
- ghalf=0.5d0*ggg2(ll)
+ gradcorr6_long(ll,j)=gradcorr6_long(ll,j)+gradcorr6ij
+ gradcorr6_long(ll,i)=gradcorr6_long(ll,i)-gradcorr6ij
+cgrad ghalf=0.5d0*ggg2(ll)
cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k)
cd ghalf=0.0d0
- gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2)
+ gradcorr6(ll,k)=gradcorr6(ll,k)+ekont*derx(ll,2,2)
gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2)
- gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2)
+ gradcorr6(ll,l)=gradcorr6(ll,l)+ekont*derx(ll,4,2)
gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2)
+ gradcorr6_long(ll,l)=gradcorr6_long(ll,l)+gradcorr6kl
+ gradcorr6_long(ll,k)=gradcorr6_long(ll,k)-gradcorr6kl
enddo
+ endif ! calc_grad
cd goto 1112
- do m=i+1,j-1
- do ll=1,3
+cgrad do m=i+1,j-1
+cgrad do ll=1,3
cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i)
- gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
- enddo
- enddo
- do m=k+1,l-1
- do ll=1,3
+cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+1,l-1
+cgrad do ll=1,3
cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k)
- gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
- enddo
- enddo
-1112 continue
- do m=i+2,j2
- do ll=1,3
- gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
- enddo
- enddo
- do m=k+2,l2
- do ll=1,3
- gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
- enddo
- enddo
+cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
+cgrad enddo
+cgrad enddo
+cgrad1112 continue
+cgrad do m=i+2,j2
+cgrad do ll=1,3
+cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+2,l2
+cgrad do ll=1,3
+cgrad gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
+cgrad enddo
+cgrad enddo
cd do iii=1,nres-3
cd write (2,*) iii,g_corr6_loc(iii)
cd enddo
- endif
eello6=ekont*eel6
cd write (2,*) 'ekont',ekont
cd write (iout,*) 'eello6',ekont*eel6
double precision function eello6_graph1(i,j,k,l,imat,swap)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
C o o C
C i i C
C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
- vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
- vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
+ vv(1)=AEAb1(1,2,imat)*b1(1,k)-AEAb1(2,2,imat)*b1(2,k)
+ vv(2)=AEAb1(1,2,imat)*b1(2,k)+AEAb1(2,2,imat)*b1(1,k)
s5=scalar2(vv(1),Dtobr2(1,i))
cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
- if (.not. calc_grad) return
+ if (calc_grad) then
if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1)
& -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i))
& -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k))
call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
- vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
- vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
+ vv(1)=AEAb1derg(1,2,imat)*b1(1,k)-AEAb1derg(2,2,imat)*b1(2,k)
+ vv(2)=AEAb1derg(1,2,imat)*b1(2,k)+AEAb1derg(2,2,imat)*b1(1,k)
if (l.eq.j+1) then
g_corr6_loc(l-1)=g_corr6_loc(l-1)
& +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
vv1(1)=pizda1(1,1)-pizda1(2,2)
vv1(2)=pizda1(1,2)+pizda1(2,1)
s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
- vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
- & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
- vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
- & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
+ vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,k)
+ & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,k)
+ vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,k)
+ & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,k)
s5=scalar2(vv(1),Dtobr2(1,i))
derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
enddo
enddo
enddo
+ endif ! calc_grad
return
end
c----------------------------------------------------------------------------
double precision function eello6_graph2(i,j,k,l,jj,kk,swap)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
include 'COMMON.GEO'
logical swap
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
- & auxvec1(2),auxvec2(1),auxmat1(2,2)
+ & auxvec1(2),auxvec2(2),auxmat1(2,2)
logical lprn
common /kutas/ lprn
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
C o o C
C \ /l\ /j\ / C
C \ / \ / \ / C
-C o| o | | o |o C
+C o| o | | o |o C
C \ j|/k\| \ |/k\|l C
C \ / \ \ / \ C
C o o C
-C i i C
-C C
+C i i C
+C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
C AL 7/4/01 s1 would occur in the sixth-order moment,
eello6_graph2=-(s2+s3+s4)
#endif
c eello6_graph2=-s3
- if (.not. calc_grad) return
C Derivatives in gamma(i-1)
+ if (calc_grad) then
if (i.gt.1) then
#ifdef MOMENT
s1=dipderg(1,jj,i)*dip(1,kk,k)
enddo
enddo
enddo
+ endif ! calc_grad
return
end
c----------------------------------------------------------------------------
double precision function eello6_graph3(i,j,k,l,jj,kk,swap)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
-C o o C
-C /l\ / \ /j\ C
+C o o C
+C /l\ / \ /j\ C
C / \ / \ / \ C
C /| o |o o| o |\ C
C j|/k\| / |/k\|l / C
C energy moment and not to the cluster cumulant.
iti=itortyp(itype(i))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
#ifdef MOMENT
s1=dip(4,jj,i)*dip(4,kk,k)
#endif
- call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
- call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
- call transpose2(EE(1,1,itk),auxmat(1,1))
+ call matvec2(AECA(1,1,1),b1(1,k+1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
+ call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
+ call transpose2(EE(1,1,k),auxmat(1,1))
call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
-cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4
+cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4,
+cd & "sum",-(s2+s3+s4)
#ifdef MOMENT
eello6_graph3=-(s1+s2+s3+s4)
#else
eello6_graph3=-(s2+s3+s4)
#endif
c eello6_graph3=-s4
- if (.not. calc_grad) return
C Derivatives in gamma(k-1)
- call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ if (calc_grad) then
+ call matvec2(AECAderg(1,1,2),b1(1,l+1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
C Derivatives in gamma(l-1)
- call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
+ call matvec2(AECAderg(1,1,1),b1(1,k+1),auxvec(1))
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
vv(2)=pizda(2,1)-pizda(1,2)
s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
endif
#endif
- call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
+ call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,k+1),
& auxvec(1))
- s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
- call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
+ s2=0.5d0*scalar2(b1(1,k),auxvec(1))
+ call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,l+1),
& auxvec(1))
- s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
+ s3=0.5d0*scalar2(b1(1,j+1),auxvec(1))
call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
& pizda(1,1))
vv(1)=pizda(1,1)+pizda(2,2)
enddo
enddo
enddo
+ endif ! calc_grad
return
end
c----------------------------------------------------------------------------
double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
& auxvec1(2),auxmat1(2,2)
logical swap
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
-C C
+C C
C Parallel Antiparallel C
C C
C o o C
C / \ / \ / \ C
C /| o |o o| o |\ C
C \ j|/k\| \ |/k\|l C
-C \ / \ \ / \ C
+C \ / \ \ / \ C
C o \ o \ C
C i i C
-C C
+C C
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C 4/7/01 AL Component s1 was removed, because it pertains to the respective
C energy moment and not to the cluster cumulant.
cd write (2,*) 'eello_graph4: wturn6',wturn6
- iti=itortyp(itype(i))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itj=itype2loc(itype(j))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itype2loc(itype(j+1))
else
- itj1=ntortyp+1
+ itj1=nloctyp
endif
- itk=itortyp(itype(k))
+ itk=itype2loc(itype(k))
if (k.lt.nres-1) then
- itk1=itortyp(itype(k+1))
+ itk1=itype2loc(itype(k+1))
else
- itk1=ntortyp+1
+ itk1=nloctyp
endif
- itl=itortyp(itype(l))
+ itl=itype2loc(itype(l))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itype2loc(itype(l+1))
else
- itl1=ntortyp+1
+ itl1=nloctyp
endif
cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1(1,1,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
call transpose2(EUg(1,1,k),auxmat(1,1))
call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
#else
eello6_graph4=-(s2+s3+s4)
#endif
- if (.not. calc_grad) return
C Derivatives in gamma(i-1)
+ if (calc_grad) then
if (i.gt.1) then
#ifdef MOMENT
if (imat.eq.1) then
#endif
s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
if (j.eq.l+1) then
- call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,j+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec1(1))
else
- call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
+ call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,l+1),auxvec1(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec1(1))
endif
call transpose2(EUgder(1,1,k),auxmat1(1,1))
call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
if (j.eq.l+1) then
call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
- & b1(1,itj1),auxvec(1))
- s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
+ & b1(1,j+1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,j),auxvec(1))
else
call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
- & b1(1,itl1),auxvec(1))
- s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
+ & b1(1,l+1),auxvec(1))
+ s3=-0.5d0*scalar2(b1(1,l),auxvec(1))
endif
call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
& pizda(1,1))
enddo
enddo
enddo
+ endif ! calc_grad
return
end
c----------------------------------------------------------------------------
double precision function eello_turn6(i,jj,kk)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
- include 'sizesclu.dat'
include 'COMMON.IOUNITS'
include 'COMMON.CHAIN'
include 'COMMON.DERIV'
& atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2)
C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to
C the respective energy moment and not to the cluster cumulant.
+ s1=0.0d0
+ s8=0.0d0
+ s13=0.0d0
+c
eello_turn6=0.0d0
j=i+4
k=i+1
l=i+3
- iti=itortyp(itype(i))
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ iti=itype2loc(itype(i))
+ itk=itype2loc(itype(k))
+ itk1=itype2loc(itype(k+1))
+ itl=itype2loc(itype(l))
+ itj=itype2loc(itype(j))
cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
cd write (2,*) 'i',i,' k',k,' j',j,' l',l
cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
#ifdef MOMENT
call transpose2(AEA(1,1,1),auxmat(1,1))
call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
- ss1=scalar2(Ub2(1,i+2),b1(1,itl))
+ ss1=scalar2(Ub2(1,i+2),b1(1,l))
s1 = (auxmat(1,1)+auxmat(2,2))*ss1
-#else
- s1 = 0.0d0
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1))
call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
- s2 = scalar2(b1(1,itk),vtemp1(1))
+ s2 = scalar2(b1(1,k),vtemp1(1))
#ifdef MOMENT
call transpose2(AEA(1,1,2),atemp(1,1))
call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
- call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
- s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
-#else
- s8=0.0d0
+ call matvec2(Ug2(1,1,i+2),dd(1,1,k+1),vtemp2(1))
+ s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
- ss13 = scalar2(b1(1,itk),vtemp4(1))
+ ss13 = scalar2(b1(1,k),vtemp4(1))
s13 = (gtemp(1,1)+gtemp(2,2))*ss13
-#else
- s13=0.0d0
#endif
c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
c s1=0.0d0
c s12=0.0d0
c s13=0.0d0
eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13)
- if (calc_grad) then
C Derivatives in gamma(i+2)
+ if (calc_grad) then
+ s1d =0.0d0
+ s8d =0.0d0
#ifdef MOMENT
call transpose2(AEA(1,1,1),auxmatd(1,1))
call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
call transpose2(AEAderg(1,1,2),atempd(1,1))
call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
- s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
-#else
- s8d=0.0d0
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
#ifdef MOMENT
call transpose2(AEA(1,1,1),auxmatd(1,1))
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
- ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
+ ss1d=scalar2(Ub2der(1,i+2),b1(1,l))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
-#else
- s1d=0.0d0
#endif
- call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(EUgder(1,1,i+2),b1(1,l),vtemp1d(1))
call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
- call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
- s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
+ call matvec2(Ug2der(1,1,i+2),dd(1,1,k+1),vtemp2d(1))
+ s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,l),vtemp2d(1))
#endif
s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
#ifdef MOMENT
call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1))
call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
s13d = (gtempd(1,1)+gtempd(2,2))*ss13
-#else
- s13d=0.0d0
#endif
c s1d=0.0d0
c s2d=0.0d0
call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1))
call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1))
s13d = (gtempd(1,1)+gtempd(2,2))*ss13
-#else
- s13d = 0.0d0
#endif
c s1d=0.0d0
c s2d=0.0d0
call transpose2(AEAderg(1,1,1),auxmatd(1,1))
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
-#else
- s1d = 0.0d0
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1d(1))
call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
call transpose2(AEA(1,1,2),atempd(1,1))
call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
- s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
-#else
- s8d = 0.0d0
+ s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,l),vtemp2(1))
#endif
call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
#ifdef MOMENT
call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
- ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ ss13d = scalar2(b1(1,k),vtemp4d(1))
s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
-#else
- s13d = 0.0d0
#endif
c s1d=0.0d0
c s2d=0.0d0
call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1))
call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
-#else
- s1d = 0.0d0
#endif
- call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
+ call matvec2(EUg(1,1,i+2),b1(1,l),vtemp1(1))
call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
& vtemp1d(1))
- s2d = scalar2(b1(1,itk),vtemp1d(1))
+ s2d = scalar2(b1(1,k),vtemp1d(1))
#ifdef MOMENT
call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
s8d = -(atempd(1,1)+atempd(2,2))*
- & scalar2(cc(1,1,itl),vtemp2(1))
-#else
- s8d = 0.0d0
+ & scalar2(cc(1,1,l),vtemp2(1))
#endif
call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
& auxmatd(1,1))
derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
& vtemp4d(1))
- ss13d = scalar2(b1(1,itk),vtemp4d(1))
+ ss13d = scalar2(b1(1,k),vtemp4d(1))
s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
enddo
l2=l-2
endif
do ll=1,3
- ggg1(ll)=eel_turn6*g_contij(ll,1)
- ggg2(ll)=eel_turn6*g_contij(ll,2)
- ghalf=0.5d0*ggg1(ll)
+cgrad ggg1(ll)=eel_turn6*g_contij(ll,1)
+cgrad ggg2(ll)=eel_turn6*g_contij(ll,2)
+cgrad ghalf=0.5d0*ggg1(ll)
cd ghalf=0.0d0
- gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf
+ gturn6ij=eel_turn6*g_contij(ll,1)+ekont*derx_turn(ll,1,1)
+ gturn6kl=eel_turn6*g_contij(ll,2)+ekont*derx_turn(ll,1,2)
+ gcorr6_turn(ll,i)=gcorr6_turn(ll,i)!+ghalf
& +ekont*derx_turn(ll,2,1)
gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1)
- gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf
+ gcorr6_turn(ll,j)=gcorr6_turn(ll,j)!+ghalf
& +ekont*derx_turn(ll,4,1)
gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1)
- ghalf=0.5d0*ggg2(ll)
+ gcorr6_turn_long(ll,j)=gcorr6_turn_long(ll,j)+gturn6ij
+ gcorr6_turn_long(ll,i)=gcorr6_turn_long(ll,i)-gturn6ij
+cgrad ghalf=0.5d0*ggg2(ll)
cd ghalf=0.0d0
- gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf
+ gcorr6_turn(ll,k)=gcorr6_turn(ll,k)!+ghalf
& +ekont*derx_turn(ll,2,2)
gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2)
- gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf
+ gcorr6_turn(ll,l)=gcorr6_turn(ll,l)!+ghalf
& +ekont*derx_turn(ll,4,2)
gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2)
+ gcorr6_turn_long(ll,l)=gcorr6_turn_long(ll,l)+gturn6kl
+ gcorr6_turn_long(ll,k)=gcorr6_turn_long(ll,k)-gturn6kl
enddo
cd goto 1112
- do m=i+1,j-1
- do ll=1,3
- gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
- enddo
- enddo
- do m=k+1,l-1
- do ll=1,3
- gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
- enddo
- enddo
-1112 continue
- do m=i+2,j2
- do ll=1,3
- gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
- enddo
- enddo
- do m=k+2,l2
- do ll=1,3
- gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
- enddo
- enddo
+cgrad do m=i+1,j-1
+cgrad do ll=1,3
+cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+1,l-1
+cgrad do ll=1,3
+cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
+cgrad enddo
+cgrad enddo
+cgrad1112 continue
+cgrad do m=i+2,j2
+cgrad do ll=1,3
+cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
+cgrad enddo
+cgrad enddo
+cgrad do m=k+2,l2
+cgrad do ll=1,3
+cgrad gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
+cgrad enddo
+cgrad enddo
cd do iii=1,nres-3
cd write (2,*) iii,g_corr6_loc(iii)
cd enddo
- endif
+ endif ! calc_grad
eello_turn6=ekont*eel_turn6
cd write (2,*) 'ekont',ekont
cd write (2,*) 'eel_turn6',ekont*eel_turn6
return
end
+
crc-------------------------------------------------
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+ subroutine Eliptransfer(eliptran)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+C this is done by Adasko
+C print *,"wchodze"
+C structure of box:
+C water
+C--bordliptop-- buffore starts
+C--bufliptop--- here true lipid starts
+C lipid
+C--buflipbot--- lipid ends buffore starts
+C--bordlipbot--buffore ends
+ eliptran=0.0
+ do i=1,nres
+C do i=1,1
+ if (itype(i).eq.ntyp1) cycle
+
+ positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,i
+C first for peptide groups
+c for each residue check if it is in lipid or lipid water border area
+ if ((positi.gt.bordlipbot)
+ &.and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+C print *, "doing sscalefor top part"
+C print *,i,sslip,fracinbuf,ssgradlip
+ else
+ eliptran=eliptran+pepliptran
+C print *,"I am in true lipid"
+ endif
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ endif
+ enddo
+C print *, "nic nie bylo w lipidzie?"
+C now multiply all by the peptide group transfer factor
+C eliptran=eliptran*pepliptran
+C now the same for side chains
+CV do i=1,1
+ do i=1,nres
+ if (itype(i).eq.ntyp1) cycle
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+C print *,positi,bordlipbot,buflipbot
+ if ((positi.gt.bordlipbot)
+ & .and.(positi.lt.bordliptop)) then
+C the energy transfer exist
+ if (positi.lt.buflipbot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-
+ &((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i)
+ &+ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1)
+ &+ssgradlip*liptranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ eliptran=eliptran+liptranene(itype(i))
+C print *,"I am in true lipid"
+ endif
+ endif ! if in lipid or buffor
+C else
+C eliptran=elpitran+0.0 ! I am in water
+ enddo
+ return
+ end
+
+
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+
SUBROUTINE MATVEC2(A1,V1,V2)
implicit real*8 (a-h,o-z)
include 'DIMENSIONS'
scalar=sc
return
end
+C-----------------------------------------------------------------------
+ double precision function sscale(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+ if(r.lt.r_cut-rlamb) then
+ sscale=1.0d0
+ else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+ gamm=(r-(r_cut-rlamb))/rlamb
+ sscale=1.0d0+gamm*gamm*(2*gamm-3.0d0)
+ else
+ sscale=0d0
+ endif
+ return
+ end
+C-----------------------------------------------------------------------
+C-----------------------------------------------------------------------
+ double precision function sscagrad(r)
+ double precision r,gamm
+ include "COMMON.SPLITELE"
+ if(r.lt.r_cut-rlamb) then
+ sscagrad=0.0d0
+ else if(r.le.r_cut.and.r.ge.r_cut-rlamb) then
+ gamm=(r-(r_cut-rlamb))/rlamb
+ sscagrad=gamm*(6*gamm-6.0d0)/rlamb
+ else
+ sscagrad=0.0d0
+ endif
+ 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
+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+1),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*y*yy(i-1)-yy(i-2)
+ enddo
+ aux=0.0d0
+ do i=m,n
+ aux=aux+x(i+1)*yy(i)*(i+1)
+C print *, x(i+1),yy(i),i
+ enddo
+ gradtschebyshev=aux
+ return
+ end
projects / unres.git / blobdiff