gshieldc_t3,gshieldc_loc_t3,gshieldx_t4,gshieldc_t4, &
gshieldc_loc_t4,gshieldx_ll,gshieldc_ll,gshieldc_loc_ll,&
grad_shield,gg_tube,gg_tube_sc,gradafm !(3,maxres)
+!-----------------------------NUCLEIC GRADIENT
+ real(kind=8),dimension(:,:),allocatable ::gradb_nucl,gradbx_nucl
! real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2)
real(kind=8),dimension(:,:),allocatable :: gel_loc,gel_loc_long,&
gcorr3_turn,gcorr4_turn,gcorr6_turn,gradb,gradbx !(3,maxres)
real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran,etube, &
Eafmforce,ethetacnstr
real(kind=8) :: ecorr,ecorr5,ecorr6,eturn6
-
+! now energies for nulceic alone parameters
+ real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
+ ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
+ ecorr3_nucl
#ifdef MPI
real(kind=8) :: weights_(n_ene) !,time_Bcast,time_Bcastw
! shielding effect varibles for MPI
if (shield_mode.eq.2) then
call set_shield_fac2
endif
+ print *,"AFTER EGB",ipot,evdw
!mc
!mc Sep-06: egb takes care of dynamic ss bonds too
!mc
! Calculate the bond-stretching energy
!
call ebond(estr)
+ print *,"EBOND",estr
! write(iout,*) "in etotal afer ebond",ipot
!
else
etube=0.0d0
endif
-
+!--------------------------------------------------------
+ call ebond_nucl(estr_nucl)
+ call ebend_nucl(ebe_nucl)
+ print *,"after ebend", ebe_nucl
#ifdef TIMING
time_enecalc=time_enecalc+MPI_Wtime()-time00
#endif
energia(23)=Eafmforce
energia(24)=ethetacnstr
energia(25)=etube
+!---------------------------------------------------------------
+ energia(26)=evdwpp
+ energia(27)=eespp
+ energia(28)=evdwpsb
+ energia(29)=eelpsb
+ energia(30)=evdwsb
+ energia(31)=eelsb
+ energia(32)=estr_nucl
+ energia(33)=ebe_nucl
+ energia(34)=esbloc
+ energia(35)=etors_nucl
+ energia(36)=etors_d_nucl
+ energia(37)=ecorr_nucl
+ energia(38)=ecorr3_nucl
+!----------------------------------------------------------------------
! Here are the energies showed per procesor if the are more processors
! per molecule then we sum it up in sum_energy subroutine
! print *," Processor",myrank," calls SUM_ENERGY"
real(kind=8) :: eel_loc,eello_turn3,eello_turn4,eturn6,ebe,escloc
real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,esccor,etot, &
eliptran,etube, Eafmforce,ethetacnstr
+ real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
+ ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
+ ecorr3_nucl
+
integer :: i
#ifdef MPI
integer :: ierr
Eafmforce=energia(23)
ethetacnstr=energia(24)
etube=energia(25)
+ estr_nucl=energia(32)
+ ebe_nucl=energia(33)
+
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 &
+wang*ebe+wtor*etors+wscloc*escloc &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
+wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube&
- +Eafmforce+ethetacnstr
+ +Eafmforce+ethetacnstr &
+ +wbond_nucl*estr_nucl+wang_nucl*ebe_nucl
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
+wang*ebe+wtor*etors+wscloc*escloc &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
+wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube&
- +Eafmforce+ethetacnstr
-
+ +Eafmforce+ethetacnstr &
+ +wbond_nucl*estr_nucl+wang_nucl*ebe_nucl
#endif
energia(0)=etot
! detecting NaNQ
real(kind=8) :: eello_turn6,eello_turn3,eello_turn4,ebe,escloc
real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran,&
etube,ethetacnstr,Eafmforce
+ real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,&
+ ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,&
+ ecorr3_nucl
etot=energia(0)
evdw=energia(1)
Eafmforce=energia(23)
ethetacnstr=energia(24)
etube=energia(25)
+ estr_nucl=energia(32)
+ ebe_nucl=energia(33)
+
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
estr,wbond,ebe,wang,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,&
edihcnstr,ethetacnstr,ebr*nss,&
- Uconst,eliptran,wliptran,Eafmforce,etube,wtube,etot
+ Uconst,eliptran,wliptran,Eafmforce,etube,wtube, & ! till now protein
+ estr_nucl,wbond_nucl,ebe_nucl,wang_nucl, &
+ etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/&
'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ &
'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ &
+ 'ESTR_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (stretching for nucleic)'/ &
+ 'EBE_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (bending for nucleic)'/ &
'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,&
ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, &
- etube,wtube,etot
+ etube,wtube, &
+ estr_nucl,wbond_nucl, ebe_nucl,wang_nucl,&
+ etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ &
'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ &
'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ &
+ 'ESTR_nucl= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching for nucleic)'/ &
+ 'EBE_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (bending for nucleic)'/ &
'ETOT= ',1pE16.6,' (total)')
#endif
return
! allocate(gacont(3,nres/4,iatsc_s:iatsc_e)) !(3,maxconts,maxres)
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
!d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
!d & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
-!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj),
!d & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
!d & (c(k,i),k=1,3),(c(k,j),k=1,3)
evdw=evdw+evdwij
! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
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)
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
-!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj),
!d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
!d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
!d & (c(k,i),k=1,3),(c(k,j),k=1,3)
! endif
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
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)
!el ind=ind+1
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),15(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & epsi,sigm,chi1,chi2,chip1,chip2,
!d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
!d & om1,om2,om12,1.0D0/dsqrt(rrij),
!el ind=0
do i=iatsc_s,iatsc_e
!C print *,"I am in EVDW",i
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
! if (i.ne.47) cycle
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
enddo! k
ELSE
!el ind=ind+1
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
! if (j.ne.78) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,&
! 1.0d0/vbld(j+nres) !d
-! write (iout,*) "i",i," j", j," itype",itype(i),itype(j)
+! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
if (rij_shift.le.0.0D0) then
evdw=1.0D20
!d write (iout,'(2(a3,i3,2x),17(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq)
return
endif
sigm=dabs(aa/bb)**(1.0D0/6.0D0)
epsi=bb**2/aa!(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j, &
+ restyp(itypi,1),i,restyp(itypj,1),j, &
epsi,sigm,chi1,chi2,chip1,chip2, &
eps1,eps2rt**2,eps3rt**2,sig,sig0ij, &
om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, &
!C print *,i,j,c(1,i),c(1,j),c(2,i),c(2,j),c(3,i),c(3,j)
! if (energy_dec) write (iout,*) &
! 'evdw',i,j,evdwij
+! print *,"ZALAMKA", evdw
! Calculate gradient components.
e1=e1*eps1*eps2rt**2*eps3rt**2
enddo ! j
enddo ! iint
enddo ! i
+! print *,"ZALAMKA", evdw
! write (iout,*) "Number of loop steps in EGB:",ind
!ccc energy_dec=.false.
return
! if (icall.eq.0) lprn=.true.
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
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)
!el ind=ind+1
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j,&
+ restyp(itypi,1),i,restyp(itypj,1),j,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
chi1,chi2,chip1,chip2,&
eps1,eps2rt**2,eps3rt**2,&
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
if (itypi.eq.ntyp1) cycle
- itypi1=iabs(itype(i+1))
+ itypi1=iabs(itype(i+1,1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
!d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
!d & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
eello_turn4=0.0d0
!el ind=0
do i=iatel_s,iatel_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=0
! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
+ if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle
!el ind=ind+1
iteli=itel(i)
itelj=itel(j)
endif
! if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
if (i.gt. nnt+2 .and. i.lt.nct+2) then
- iti = itortyp(itype(i-2))
+ iti = itortyp(itype(i-2,1))
else
iti=ntortyp+1
endif
! if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
if (i.gt. nnt+1 .and. i.lt.nct+1) then
- iti1 = itortyp(itype(i-1))
+ iti1 = itortyp(itype(i-1,1))
else
iti1=ntortyp+1
endif
-! print *,iti,i,"iti",iti1,itype(i-1),itype(i-2)
+! print *,iti,i,"iti",iti1,itype(i-1,1),itype(i-2,1)
!d write (iout,*) '*******i',i,' iti1',iti
!d write (iout,*) 'b1',b1(:,iti)
!d write (iout,*) 'b2',b2(:,iti)
enddo
! 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))
+ if (itype(i-1,1).le.ntyp) then
+ iti1 = itortyp(itype(i-1,1))
else
iti1=ntortyp+1
endif
#endif
#endif
!d do i=1,nres
-!d iti = itortyp(itype(i))
+!d iti = itortyp(itype(i,1))
!d write (iout,*) i
!d do j=1,2
!d write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
! print *,"before iturn3 loop"
do i=iturn3_start,iturn3_end
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 &
- .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 &
+ .or. itype(i+2,1).eq.ntyp1 .or. itype(i+3,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 &
- .or. itype(i+3).eq.ntyp1 &
- .or. itype(i+4).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 &
+ .or. itype(i+3,1).eq.ntyp1 &
+ .or. itype(i+4,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_conti=num_cont_hb(i)
call eelecij(i,i+3,ees,evdw1,eel_loc)
- if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1) &
+ if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
call eturn4(i,eello_turn4)
num_cont_hb(i)=num_conti
enddo ! i
! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
!
do i=iatel_s,iatel_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
-! write (iout,*) i,j,itype(i),itype(j)
- if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1) cycle
+! write (iout,*) i,j,itype(i,1),itype(j,1)
+ if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle
call eelecij(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
a32=a32*fac
a33=a33*fac
!d write (iout,'(4i5,4f10.5)')
-!d & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
+!d & i,itortyp(itype(i,1)),j,itortyp(itype(j,1)),a22,a23,a32,a33
!d write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
!d write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i),
!d & uy(:,j),uz(:,j)
a_temp(1,2)=a23
a_temp(2,1)=a32
a_temp(2,2)=a33
- iti1=itortyp(itype(i+1))
- iti2=itortyp(itype(i+2))
- iti3=itortyp(itype(i+3))
+ iti1=itortyp(itype(i+1,1))
+ iti2=itortyp(itype(i+2,1))
+ iti3=itortyp(itype(i+3,1))
! 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))
!d print '(a)','Enter ESCP'
!d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- if (itype(j).eq.ntyp1) cycle
- itypj=iabs(itype(j))
+ if (itype(j,1).eq.ntyp1) cycle
+ itypj=iabs(itype(j,1))
! Uncomment following three lines for SC-p interactions
! xj=c(1,nres+j)-xi
! yj=c(2,nres+j)-yi
!d print '(a)','Enter ESCP'
!d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
if (itypj.eq.ntyp1) cycle
! Uncomment following three lines for SC-p interactions
! xj=c(1,nres+j)-xi
! 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
if (.not.dyn_ss .and. i.le.nss) then
! 15/02/13 CC dynamic SSbond - additional check
- if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. &
- iabs(itype(jjj)).eq.1) then
+ if (ii.gt.nres .and. iabs(itype(iii,1)).eq.1 .and. &
+ iabs(itype(jjj,1)).eq.1) then
call ssbond_ene(iii,jjj,eij)
ehpb=ehpb+2*eij
!d write (iout,*) "eij",eij
deltat1,deltat2,deltat12,ed,pom1,pom2,eom1,eom2,eom12,&
cosphi,ggk
- itypi=iabs(itype(i))
+ itypi=iabs(itype(i,1))
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
dzi=dc_norm(3,nres+i)
! dsci_inv=dsc_inv(itypi)
dsci_inv=vbld_inv(nres+i)
- itypj=iabs(itype(j))
+ itypj=iabs(itype(j,1))
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(nres+j)
xj=c(1,nres+j)-xi
! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres)
do i=ibondp_start,ibondp_end
- if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle
- if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
+ if (itype(i-1,1).eq.ntyp1 .and. itype(i,1).eq.ntyp1) cycle
+ if (itype(i-1,1).eq.ntyp1 .or. itype(i,1).eq.ntyp1) then
!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) &
! endif
enddo
estr=0.5d0*AKP*estr+estr1
+! print *,"estr_bb",estr,AKP
!
! 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
!
do i=ibond_start,ibond_end
- iti=iabs(itype(i))
+ iti=iabs(itype(i,1))
+ if (iti.eq.0) print *,"WARNING WRONG SETTTING",i
if (iti.ne.10 .and. iti.ne.ntyp1) then
nbi=nbondterm(iti)
if (nbi.eq.1) then
"estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff,&
AKSC(1,iti),AKSC(1,iti)*diff*diff
estr=estr+0.5d0*AKSC(1,iti)*diff*diff
+! print *,"estr_sc",estr
do j=1,3
gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
enddo
usumsqder=usumsqder+ud(j)*uprod2
enddo
estr=estr+uprod/usum
+! print *,"estr_sc",estr,i
+
if (energy_dec) write (iout,*) &
"estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff,&
- AKSC(1,iti),AKSC(1,iti)*diff*diff
+ AKSC(1,iti),uprod/usum
do j=1,3
gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
enddo
etheta=0.0D0
! write (*,'(a,i2)') 'EBEND ICG=',icg
do i=ithet_start,ithet_end
- if (itype(i-1).eq.ntyp1) cycle
+ if (itype(i-1,1).eq.ntyp1) cycle
! Zero the energy function and its derivative at 0 or pi.
call splinthet(theta(i),0.5d0*delta,ss,ssd)
- it=itype(i-1)
- 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))
+ it=itype(i-1,1)
+ ichir1=isign(1,itype(i-2,1))
+ ichir2=isign(1,itype(i,1))
+ if (itype(i-2,1).eq.10) ichir1=isign(1,itype(i-1,1))
+ if (itype(i,1).eq.10) ichir2=isign(1,itype(i-1,1))
+ if (itype(i-1,1).eq.10) then
+ itype1=isign(10,itype(i-2,1))
+ ichir11=isign(1,itype(i-2,1))
+ ichir12=isign(1,itype(i-2,1))
+ itype2=isign(10,itype(i,1))
+ ichir21=isign(1,itype(i,1))
+ ichir22=isign(1,itype(i,1))
endif
- if (i.gt.3 .and. itype(i-2).ne.ntyp1) then
+ if (i.gt.3 .and. itype(i-2,1).ne.ntyp1) then
#ifdef OSF
phii=phi(i)
if (phii.ne.phii) phii=150.0
y(1)=0.0D0
y(2)=0.0D0
endif
- if (i.lt.nres .and. itype(i).ne.ntyp1) then
+ if (i.lt.nres .and. itype(i,1).ne.ntyp1) then
#ifdef OSF
phii1=phi(i+1)
if (phii1.ne.phii1) phii1=150.0
etheta=0.0D0
do i=ithet_start,ithet_end
- if (itype(i-1).eq.ntyp1) cycle
- if (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
+ if (itype(i-1,1).eq.ntyp1) cycle
+ if (itype(i-2,1).eq.ntyp1.or.itype(i,1).eq.ntyp1) cycle
+ if (iabs(itype(i+1,1)).eq.20) iblock=2
+ if (iabs(itype(i+1,1)).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-1,1)))
do k=1,nntheterm
coskt(k)=dcos(k*theti2)
sinkt(k)=dsin(k*theti2)
enddo
- if (i.gt.3 .and. itype(max0(i-3,1)).ne.ntyp1) then
+ if (i.gt.3 .and. itype(max0(i-3,1),1).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-2,1)))
! propagation of chirality for glycine type
do k=1,nsingle
cosph1(k)=dcos(k*phii)
enddo
else
phii=0.0d0
- ityp1=ithetyp(itype(i-2))
+ ityp1=ithetyp(itype(i-2,1))
do k=1,nsingle
cosph1(k)=0.0d0
sinph1(k)=0.0d0
enddo
endif
- if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
+ if (i.lt.nres .and. itype(i+1,1).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,1)))
do k=1,nsingle
cosph2(k)=dcos(k*phii1)
sinph2(k)=dsin(k*phii1)
enddo
else
phii1=0.0d0
- ityp3=ithetyp(itype(i))
+ ityp3=ithetyp(itype(i,1))
do k=1,nsingle
cosph2(k)=0.0d0
sinph2(k)=0.0d0
escloc=0.0D0
! write (iout,'(a)') 'ESC'
do i=loc_start,loc_end
- it=itype(i)
+ it=itype(i,1)
if (it.eq.ntyp1) cycle
if (it.eq.10) goto 1
nlobit=nlob(iabs(it))
delta=0.02d0*pi
escloc=0.0D0
do i=loc_start,loc_end
- if (itype(i).eq.ntyp1) cycle
+ if (itype(i,1).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=iabs(itype(i))
+ it=iabs(itype(i,1))
if (it.eq.10) goto 1
!
! 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)*dsign(1.0d0,dfloat(itype(i)))
+ z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i,1)))
enddo
! write (2,*) "i",i
! write (2,*) "x_prime",(x_prime(j),j=1,3)
! Compute the energy of the ith side cbain
!
! write (2,*) "xx",xx," yy",yy," zz",zz
- it=iabs(itype(i))
+ it=iabs(itype(i,1))
do j = 1,65
x(j) = sc_parmin(j,it)
enddo
!c diagnostics - remove later
xx1 = dcos(alph(2))
yy1 = dsin(alph(2))*dcos(omeg(2))
- zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
+ zz1 = -dsign(1.0,dfloat(itype(i,1)))*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
! & dscp1,dscp2,sumene
! sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
escloc = escloc + sumene
-! write (2,*) "i",i," escloc",sumene,escloc,it,itype(i)
+! write (2,*) "i",i," escloc",sumene,escloc,it,itype(i,1)
! & ,zz,xx,yy
!#define DEBUG
#ifdef DEBUG
!
! Compute the gradient of esc
!
-! zz=zz*dsign(1.0,dfloat(itype(i)))
+! zz=zz*dsign(1.0,dfloat(itype(i,1)))
pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
+(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6) &
+(pom1+pom2)*pom_dx
#ifdef DEBUG
- write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i)
+ write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i,1)
#endif
!
sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
+(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6) &
+(pom1-pom2)*pom_dy
#ifdef DEBUG
- write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i)
+ write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i,1)
#endif
!
de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy &
+x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6) &
+ ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
#ifdef DEBUG
- write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i)
+ write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i,1)
#endif
!
de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6) &
-0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6) &
+pom1*pom_dt1+pom2*pom_dt2
#ifdef DEBUG
- write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i)
+ write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i,1)
#endif
!
!
dZZ_Ci(k)=0.0d0
do j=1,3
dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1) &
- *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+ *dsign(1.0d0,dfloat(itype(i,1)))*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)
+ *dsign(1.0d0,dfloat(itype(i,1)))*dC_norm(j,i+nres)
enddo
dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
etors=0.0D0
do i=iphi_start,iphi_end
etors_ii=0.0D0
- 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))
+ if (itype(i-2,1).eq.ntyp1.or. itype(i-1,1).eq.ntyp1 &
+ .or. itype(i,1).eq.ntyp1) cycle
+ itori=itortyp(itype(i-2,1))
+ itori1=itortyp(itype(i-1,1))
phii=phi(i)
gloci=0.0D0
! Proline-Proline pair is a special case...
'etor',i,etors_ii
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,&
+ restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,itori,itori1,&
(v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
! write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
! lprn=.true.
etors=0.0D0
do i=iphi_start,iphi_end
- if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 &
- .or. itype(i-3).eq.ntyp1 &
- .or. itype(i).eq.ntyp1) cycle
+ if (itype(i-2,1).eq.ntyp1 .or. itype(i-1,1).eq.ntyp1 &
+ .or. itype(i-3,1).eq.ntyp1 &
+ .or. itype(i,1).eq.ntyp1) cycle
etors_ii=0.0D0
- if (iabs(itype(i)).eq.20) then
+ if (iabs(itype(i,1)).eq.20) then
iblock=2
else
iblock=1
endif
- itori=itortyp(itype(i-2))
- itori1=itortyp(itype(i-1))
+ itori=itortyp(itype(i-2,1))
+ itori1=itortyp(itype(i-1,1))
phii=phi(i)
gloci=0.0D0
! Regular cosine and sine terms
'etor',i,etors_ii-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,&
+ restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,itori,itori1,&
(v1(j,itori,itori1,iblock),j=1,6),&
(v2(j,itori,itori1,iblock),j=1,6)
gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci
! write(iout,*) "a tu??"
do i=iphid_start,iphid_end
etors_d_ii=0.0D0
- if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 &
- .or. itype(i-3).eq.ntyp1 &
- .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
- itori=itortyp(itype(i-2))
- itori1=itortyp(itype(i-1))
- itori2=itortyp(itype(i))
+ if (itype(i-2,1).eq.ntyp1 .or. itype(i-1,1).eq.ntyp1 &
+ .or. itype(i-3,1).eq.ntyp1 &
+ .or. itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
+ itori=itortyp(itype(i-2,1))
+ itori1=itortyp(itype(i-1,1))
+ itori2=itortyp(itype(i,1))
phii=phi(i)
phii1=phi(i+1)
gloci1=0.0D0
gloci2=0.0D0
iblock=1
- if (iabs(itype(i+1)).eq.20) iblock=2
+ if (iabs(itype(i+1,1)).eq.20) iblock=2
! Regular cosine and sine terms
do j=1,ntermd_1(itori,itori1,itori2,iblock)
! write (iout,*) "EBACK_SC_COR",itau_start,itau_end
esccor=0.0D0
do i=itau_start,itau_end
- if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
+ if ((itype(i-2,1).eq.ntyp1).or.(itype(i-1,1).eq.ntyp1)) cycle
esccor_ii=0.0D0
- isccori=isccortyp(itype(i-2))
- isccori1=isccortyp(itype(i-1))
+ isccori=isccortyp(itype(i-2,1))
+ isccori1=isccortyp(itype(i-1,1))
! write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1)
phii=phi(i)
! 2 = Ca...Ca...Ca...SC
! 3 = SC...Ca...Ca...SCi
gloci=0.0D0
- 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)) &
+ if (((intertyp.eq.3).and.((itype(i-2,1).eq.10).or. &
+ (itype(i-1,1).eq.10).or.(itype(i-2,1).eq.ntyp1).or. &
+ (itype(i-1,1).eq.ntyp1))) &
+ .or. ((intertyp.eq.1).and.((itype(i-2,1).eq.10) &
+ .or.(itype(i-2,1).eq.ntyp1).or.(itype(i-1,1).eq.ntyp1) &
+ .or.(itype(i,1).eq.ntyp1))) &
+ .or.((intertyp.eq.2).and.((itype(i-1,1).eq.10).or. &
+ (itype(i-1,1).eq.ntyp1).or.(itype(i-2,1).eq.ntyp1).or. &
+ (itype(i-3,1).eq.ntyp1)))) cycle
+ if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1,1).eq.ntyp1)) cycle
+ if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres,1).eq.ntyp1)) &
cycle
do j=1,nterm_sccor(isccori,isccori1)
v1ij=v1sccor(j,intertyp,isccori,isccori1)
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,isccori,isccori1,&
+ restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,isccori,isccori1,&
(v1sccor(j,intertyp,isccori,isccori1),j=1,6),&
(v2sccor(j,intertyp,isccori,isccori1),j=1,6)
gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
allocate(dipderx(3,5,4,maxconts,nres))
!
- iti1 = itortyp(itype(i+1))
+ iti1 = itortyp(itype(i+1,1))
if (j.lt.nres-1) then
- itj1 = itortyp(itype(j+1))
+ itj1 = itortyp(itype(j+1,1))
else
itj1=ntortyp+1
endif
if (l.eq.j+1) then
! parallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itortyp(itype(i,1))
else
iti=ntortyp+1
endif
- itk1=itortyp(itype(k+1))
- itj=itortyp(itype(j))
+ itk1=itortyp(itype(k+1,1))
+ itj=itortyp(itype(j,1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itortyp(itype(l+1,1))
else
itl1=ntortyp+1
endif
else
! Antiparallel orientation of the two CA-CA-CA frames.
if (i.gt.1) then
- iti=itortyp(itype(i))
+ iti=itortyp(itype(i,1))
else
iti=ntortyp+1
endif
- itk1=itortyp(itype(k+1))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk1=itortyp(itype(k+1,1))
+ itl=itortyp(itype(l,1))
+ itj=itortyp(itype(j,1))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itortyp(itype(j+1,1))
else
itj1=ntortyp+1
endif
!d write (iout,*)
!d & 'EELLO5: Contacts have occurred for peptide groups',i,j,
!d & ' and',k,l
- itk=itortyp(itype(k))
- itl=itortyp(itype(l))
- itj=itortyp(itype(j))
+ itk=itortyp(itype(k,1))
+ itl=itortyp(itype(l,1))
+ itj=itortyp(itype(j,1))
eello5_1=0.0d0
eello5_2=0.0d0
eello5_3=0.0d0
! i i C
! C
!CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
- itk=itortyp(itype(k))
+ itk=itortyp(itype(k,1))
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))
!
! 4/7/01 AL Component s1 was removed, because it pertains to the respective
! energy moment and not to the cluster cumulant.
- iti=itortyp(itype(i))
+ iti=itortyp(itype(i,1))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itortyp(itype(j+1,1))
else
itj1=ntortyp+1
endif
- itk=itortyp(itype(k))
- itk1=itortyp(itype(k+1))
+ itk=itortyp(itype(k,1))
+ itk1=itortyp(itype(k+1,1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itortyp(itype(l+1,1))
else
itl1=ntortyp+1
endif
! 4/7/01 AL Component s1 was removed, because it pertains to the respective
! energy moment and not to the cluster cumulant.
!d write (2,*) 'eello_graph4: wturn6',wturn6
- iti=itortyp(itype(i))
- itj=itortyp(itype(j))
+ iti=itortyp(itype(i,1))
+ itj=itortyp(itype(j,1))
if (j.lt.nres-1) then
- itj1=itortyp(itype(j+1))
+ itj1=itortyp(itype(j+1,1))
else
itj1=ntortyp+1
endif
- itk=itortyp(itype(k))
+ itk=itortyp(itype(k,1))
if (k.lt.nres-1) then
- itk1=itortyp(itype(k+1))
+ itk1=itortyp(itype(k+1,1))
else
itk1=ntortyp+1
endif
- itl=itortyp(itype(l))
+ itl=itortyp(itype(l,1))
if (l.lt.nres-1) then
- itl1=itortyp(itype(l+1))
+ itl1=itortyp(itype(l+1,1))
else
itl1=ntortyp+1
endif
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=itortyp(itype(i,1))
+ itk=itortyp(itype(k,1))
+ itk1=itortyp(itype(k+1,1))
+ itl=itortyp(itype(l,1))
+ itj=itortyp(itype(j,1))
!d write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
!d write (2,*) 'i',i,' k',k,' j',j,' l',l
!d if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
+wturn3*gshieldc_t3(j,i)&
+wturn4*gshieldc_t4(j,i)&
+wel_loc*gshieldc_ll(j,i)&
- +wtube*gg_tube(j,i)
-
-
-
+ +wtube*gg_tube(j,i) &
+ +wbond_nucl*gradb_nucl(j,i)
enddo
enddo
#else
+wcorr*gshieldc_ec(j,i) &
+wturn4*gshieldc_t4(j,i) &
+wel_loc*gshieldc_ll(j,i)&
- +wtube*gg_tube(j,i)
-
-
+ +wtube*gg_tube(j,i) &
+ +wbond_nucl*gradb_nucl(j,i)
enddo
enddo
+wturn4*gshieldc_loc_t4(j,i) &
+wel_loc*gshieldc_ll(j,i) &
+wel_loc*gshieldc_loc_ll(j,i) &
- +wtube*gg_tube(j,i)
+ +wtube*gg_tube(j,i) &
+ +wbond_nucl*gradb_nucl(j,i)
+
#else
+wturn4*gshieldc_loc_t4(j,i) &
+wel_loc*gshieldc_ll(j,i) &
+wel_loc*gshieldc_loc_ll(j,i) &
- +wtube*gg_tube(j,i)
+ +wtube*gg_tube(j,i) &
+ +wbond_nucl*gradb_nucl(j,i)
+
+wturn3*gshieldx_t3(j,i) &
+wturn4*gshieldx_t4(j,i) &
+wel_loc*gshieldx_ll(j,i)&
- +wtube*gg_tube_sc(j,i)
+ +wtube*gg_tube_sc(j,i) &
+ +wbond_nucl*gradbx_nucl(j,i)
+
enddo
! include 'COMMON.CALC'
! include 'COMMON.IOUNITS'
real(kind=8), dimension(3) :: dcosom1,dcosom2
-
+! print *,"wchodze"
eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
! Derivatives in alpha and omega:
!
do i=2,nres-1
-! dsci=dsc(itype(i))
+! dsci=dsc(itype(i,1))
dsci=vbld(i+nres)
#ifdef OSF
alphi=alph(i)
! write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
!d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
!d & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
! write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
!d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
!d & 'iend=',iend(i,iint)
do j=istart(i,iint),iend(i,iint)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
-!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj),
!d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
!d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
!d & (c(k,i),k=1,3),(c(k,j),k=1,3)
! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
xj=c(1,nres+j)-xi
yj=c(2,nres+j)-yi
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
-!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
+!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj),
!d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
!d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
!d & (c(k,i),k=1,3),(c(k,j),k=1,3)
! endif
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),15(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & epsi,sigm,chi1,chi2,chip1,chip2,
!d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
!d & om1,om2,om12,1.0D0/dsqrt(rrij),
! endif
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
!d write (iout,'(2(a3,i3,2x),15(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & epsi,sigm,chi1,chi2,chip1,chip2,
!d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
!d & om1,om2,om12,1.0D0/dsqrt(rrij),
! if (icall.eq.0) lprn=.false.
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
ELSE
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
! & 1.0d0/vbld(j+nres)
-! write (iout,*) "i",i," j", j," itype",itype(i),itype(j)
+! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
if (rij_shift.le.0.0D0) then
evdw=1.0D20
!d write (iout,'(2(a3,i3,2x),17(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq)
return
endif
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j,&
+ restyp(itypi,1),i,restyp(itypj,1),j,&
epsi,sigm,chi1,chi2,chip1,chip2,&
eps1,eps2rt**2,eps3rt**2,sig,sig0ij,&
om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,&
! if (icall.eq.0) lprn=.false.
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
! 'evdw',i,j,evdwij,' ss'
ELSE
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
! & 1.0d0/vbld(j+nres)
-! write (iout,*) "i",i," j", j," itype",itype(i),itype(j)
+! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1)
sig0ij=sigma(itypi,itypj)
chi1=chi(itypi,itypj)
chi2=chi(itypj,itypi)
if (rij_shift.le.0.0D0) then
evdw=1.0D20
!d write (iout,'(2(a3,i3,2x),17(0pf7.3))')
-!d & restyp(itypi),i,restyp(itypj),j,
+!d & restyp(itypi,1),i,restyp(itypj,1),j,
!d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq)
return
endif
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j,&
+ restyp(itypi,1),i,restyp(itypj,1),j,&
epsi,sigm,chi1,chi2,chip1,chip2,&
eps1,eps2rt**2,eps3rt**2,sig,sig0ij,&
om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,&
! if (icall.eq.0) lprn=.true.
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j,&
+ restyp(itypi,1),i,restyp(itypj,1),j,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
chi1,chi2,chip1,chip2,&
eps1,eps2rt**2,eps3rt**2,&
! if (icall.eq.0) lprn=.true.
!el ind=0
do i=iatsc_s,iatsc_e
- itypi=itype(i)
+ itypi=itype(i,1)
if (itypi.eq.ntyp1) cycle
- itypi1=itype(i+1)
+ itypi1=itype(i+1,1)
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)
!el ind=ind+1
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! dscj_inv=dsc_inv(itypj)
dscj_inv=vbld_inv(j+nres)
sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
- restyp(itypi),i,restyp(itypj),j,&
+ restyp(itypi,1),i,restyp(itypj,1),j,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
chi1,chi2,chip1,chip2,&
eps1,eps2rt**2,eps3rt**2,&
! Loop over i,i+2 and i,i+3 pairs of the peptide groups
!
do i=iturn3_start,iturn3_end
- if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1 &
- .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1.or. itype(i+1,1).eq.ntyp1 &
+ .or. itype(i+2,1).eq.ntyp1 .or. itype(i+3,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
num_cont_hb(i)=num_conti
enddo
do i=iturn4_start,iturn4_end
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 &
- .or. itype(i+3).eq.ntyp1 &
- .or. itype(i+4).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 &
+ .or. itype(i+3,1).eq.ntyp1 &
+ .or. itype(i+4,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
num_conti=num_cont_hb(i)
call eelecij_scale(i,i+3,ees,evdw1,eel_loc)
- if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1) &
+ if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) &
call eturn4(i,eello_turn4)
num_cont_hb(i)=num_conti
enddo ! i
! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
!
do i=iatel_s,iatel_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
do j=ielstart(i),ielend(i)
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
+ if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle
call eelecij_scale(i,j,ees,evdw1,eel_loc)
enddo ! j
num_cont_hb(i)=num_conti
a32=a32*fac
a33=a33*fac
!d write (iout,'(4i5,4f10.5)')
-!d & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
+!d & i,itortyp(itype(i,1)),j,itortyp(itype(j,1)),a22,a23,a32,a33
!d write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
!d write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i),
!d & uy(:,j),uz(:,j)
! & " iatel_e_vdw",iatel_e_vdw
call flush(iout)
do i=iatel_s_vdw,iatel_e_vdw
- if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1.or. itype(i+1,1).eq.ntyp1) cycle
dxi=dc(1,i)
dyi=dc(2,i)
dzi=dc(3,i)
! & ' ielend',ielend_vdw(i)
call flush(iout)
do j=ielstart_vdw(i),ielend_vdw(i)
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle
+ if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle
!el ind=ind+1
iteli=itel(i)
itelj=itel(j)
!d print '(a)','Enter ESCP'
!d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! Uncomment following three lines for SC-p interactions
! xj=c(1,nres+j)-xi
!d print '(a)','Enter ESCP'
!d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e
do i=iatscp_s,iatscp_e
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
iteli=itel(i)
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
do iint=1,nscp_gr(i)
do j=iscpstart(i,iint),iscpend(i,iint)
- itypj=itype(j)
+ itypj=itype(j,1)
if (itypj.eq.ntyp1) cycle
! Uncomment following three lines for SC-p interactions
! xj=c(1,nres+j)-xi
enddo
if (n.le.nphi+ntheta) goto 10
do i=2,nres-1
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
galphai=0.0D0
gomegai=0.0D0
do k=1,3
gg_tube(j,i)=0.0d0
gg_tube_sc(j,i)=0.0d0
gradafm(j,i)=0.0d0
+ gradb_nucl(j,i)=0.0d0
+ gradbx_nucl(j,i)=0.0d0
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo
do j=1,3
dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/&
vbld(i-1)
- if (itype(i-1).ne.ntyp1) dtheta(j,1,i)=-dcostheta(j,1,i)/sint
+ if (itype(i-1,1).ne.ntyp1) dtheta(j,1,i)=-dcostheta(j,1,i)/sint
dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/&
vbld(i)
- if (itype(i-1).ne.ntyp1) dtheta(j,2,i)=-dcostheta(j,2,i)/sint
+ if (itype(i-1,1).ne.ntyp1) dtheta(j,2,i)=-dcostheta(j,2,i)/sint
enddo
enddo
#if defined(MPI) && defined(PARINTDER)
#else
do i=3,nres
#endif
- if ((itype(i-1).ne.10).and.(itype(i-1).ne.ntyp1)) then
+ if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1)) then
cost1=dcos(omicron(1,i))
sint1=sqrt(1-cost1*cost1)
cost2=dcos(omicron(2,i))
dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) &
+cost2*(-dc_norm(j,i-1+nres)))/ &
vbld(i-1+nres)
-! write(iout,*) "vbld", i,itype(i),vbld(i-1+nres)
+! write(iout,*) "vbld", i,itype(i,1),vbld(i-1+nres)
domicron(j,2,2,i)=-1/sint2*dcosomicron(j,2,2,i)
enddo
endif
#else
do i=4,nres
#endif
-! if (itype(i-1).eq.21 .or. itype(i-2).eq.21 ) cycle
+! if (itype(i-1,1).eq.21 .or. itype(i-2,1).eq.21 ) cycle
! the conventional case
sint=dsin(theta(i))
sint1=dsin(theta(i-1))
ctgt=cost/sint
ctgt1=cost1/sint1
cosg_inv=1.0d0/cosg
- if (itype(i-1).ne.ntyp1 .and. itype(i-2).ne.ntyp1) then
+ if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) &
-(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2)
dphi(j,1,i)=cosg_inv*dsinphi(j,1,i)
! Obtaining the gamma derivatives from cosine derivative
else
do j=1,3
- if (itype(i-1).ne.ntyp1 .and. itype(i-2).ne.ntyp1) then
+ if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then
dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* &
dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* &
dc_norm(j,i-3))/vbld(i-2)
do i=3,nres
!elwrite(iout,*) " vecpr",i,nres
#endif
- if ((itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10)) cycle
-! if ((itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10).or.
-! & (itype(i-1).eq.ntyp1).or.(itype(i).eq.ntyp1)) cycle
+ if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
+! if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10).or.
+! & (itype(i-1,1).eq.ntyp1).or.(itype(i,1).eq.ntyp1)) cycle
!c dtauangle(j,intertyp,dervityp,residue number)
!c INTERTYP=1 SC...Ca...Ca..Ca
! the conventional case
#else
do i=4,nres
#endif
- if ((itype(i-1).eq.ntyp1).or.(itype(i-1).eq.10).or. &
- (itype(i-2).eq.ntyp1).or.(itype(i-3).eq.ntyp1)) cycle
+ if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
+ (itype(i-2,1).eq.ntyp1).or.(itype(i-3,1).eq.ntyp1)) cycle
! the conventional case
sint=dsin(omicron(1,i))
sint1=dsin(theta(i-1))
do i=3,nres
#endif
! the conventional case
- if ((itype(i-1).eq.ntyp1).or.(itype(i-1).eq.10).or. &
- (itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10)) cycle
+ if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. &
+ (itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle
sint=dsin(omicron(1,i))
sint1=dsin(omicron(2,i-1))
sing=dsin(tauangle(3,i))
#else
do i=2,nres-1
#endif
- if(itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1))))
fac6=fac5/vbld(i)
fac7=fac5*fac5
write (iout,*) &
"Analytical (upper) and numerical (lower) gradient of alpha"
do i=2,nres-1
- if(itype(i).ne.10) then
+ if(itype(i,1).ne.10) then
do j=1,3
dcji=dc(j,i-1)
dc(j,i-1)=dcji+aincr
write (iout,*) &
"Analytical (upper) and numerical (lower) gradient of omega"
do i=2,nres-1
- if(itype(i).ne.10) then
+ if(itype(i,1).ne.10) then
do j=1,3
dcji=dc(j,i-1)
dc(j,i-1)=dcji+aincr
(cref(3,jl,kkk)-cref(3,il,kkk))**2)
dij=dist(il,jl)
qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
- if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
nl=nl+1
d0ijCM=dsqrt( &
(cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
(cref(3,jl,kkk)-cref(3,il,kkk))**2)
dij=dist(il,jl)
qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2)
- if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
nl=nl+1
d0ijCM=dsqrt( &
(cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
dqwol(k,jl)=dqwol(k,jl)-ddqij
enddo
- if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
nl=nl+1
d0ijCM=dsqrt( &
(cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
dqwol(k,il)=dqwol(k,il)+ddqij
dqwol(k,jl)=dqwol(k,jl)-ddqij
enddo
- if (itype(il).ne.10 .or. itype(jl).ne.10) then
+ if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then
nl=nl+1
d0ijCM=dsqrt( &
(cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ &
!el allocate(dyn_ssbond_ij(iatsc_s:iatsc_e,nres))
!el allocate(dyn_ssbond_ij(0:nres+4,nres))
- itypi=itype(i)
+ itypi=itype(i,1)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=vbld_inv(i+nres)
- itypj=itype(j)
+ itypj=itype(j,1)
xj=c(1,nres+j)-c(1,nres+i)
yj=c(2,nres+j)-c(2,nres+i)
zj=c(3,nres+j)-c(3,nres+i)
j=resj
k=resk
!C write(iout,*) resi,resj,resk
- itypi=itype(i)
+ itypi=itype(i,1)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
- itypj=itype(j)
+ itypj=itype(j,1)
xj=c(1,nres+j)
yj=c(2,nres+j)
zj=c(3,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
dscj_inv=vbld_inv(j+nres)
- itypk=itype(k)
+ itypk=itype(k,1)
xk=c(1,nres+k)
yk=c(2,nres+k)
zk=c(3,nres+k)
! print *, "I am in eliptran"
do i=ilip_start,ilip_end
!C do i=1,1
- if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1).or.(i.eq.nres))&
+ if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1).or.(i.eq.nres))&
cycle
positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
enddo
! here starts the side chain transfer
do i=ilip_start,ilip_end
- if (itype(i).eq.ntyp1) cycle
+ if (itype(i,1).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 lipbufthick is thickenes of lipid buffore
sslip=sscalelip(fracinbuf)
ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
- eliptran=eliptran+sslip*liptranene(itype(i))
+ eliptran=eliptran+sslip*liptranene(itype(i,1))
gliptranx(3,i)=gliptranx(3,i) &
- +ssgradlip*liptranene(itype(i))
+ +ssgradlip*liptranene(itype(i,1))
gliptranc(3,i-1)= gliptranc(3,i-1) &
- +ssgradlip*liptranene(itype(i))
+ +ssgradlip*liptranene(itype(i,1))
!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))
+ eliptran=eliptran+sslip*liptranene(itype(i,1))
gliptranx(3,i)=gliptranx(3,i) &
- +ssgradlip*liptranene(itype(i))
+ +ssgradlip*liptranene(itype(i,1))
gliptranc(3,i-1)= gliptranc(3,i-1) &
- +ssgradlip*liptranene(itype(i))
+ +ssgradlip*liptranene(itype(i,1))
!C print *, "doing sscalefor top part",sslip,fracinbuf
else
- eliptran=eliptran+liptranene(itype(i))
+ eliptran=eliptran+liptranene(itype(i,1))
!C print *,"I am in true lipid"
endif
endif ! if in lipid or buffor
!C for UNRES
do i=itube_start,itube_end
!C lets ommit dummy atoms for now
- if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+ if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle
!C now calculate distance from center of tube and direction vectors
xmin=boxxsize
ymin=boxysize
do i=itube_start,itube_end
!C Lets not jump over memory as we use many times iti
- iti=itype(i)
+ iti=itype(i,1)
!C lets ommit dummy atoms for now
if ((iti.eq.ntyp1) &
!C in UNRES uncomment the line below as GLY has no side-chain...
do i=itube_start,itube_end
!C lets ommit dummy atoms for now
- if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+ if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle
!C now calculate distance from center of tube and direction vectors
!C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
!C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
!C lipbufthick is thickenes of lipid buffore
sstube=sscalelip(fracinbuf)
ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
-!C print *,ssgradtube, sstube,tubetranene(itype(i))
+!C print *,ssgradtube, sstube,tubetranene(itype(i,1))
enetube(i)=enetube(i)+sstube*tubetranenepep
!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C gg_tube(3,i-1)= gg_tube(3,i-1)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C print *,"doing sccale for lower part"
elseif (positi.gt.buftubetop) then
fracinbuf=1.0d0- &
ssgradtube=sscagradlip(fracinbuf)/tubebufthick
enetube(i)=enetube(i)+sstube*tubetranenepep
!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C gg_tube(3,i-1)= gg_tube(3,i-1)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C print *, "doing sscalefor top part",sslip,fracinbuf
else
sstube=1.0d0
!C print *,gg_tube(1,0),"TU"
do i=itube_start,itube_end
!C Lets not jump over memory as we use many times iti
- iti=itype(i)
+ iti=itype(i,1)
!C lets ommit dummy atoms for now
if ((iti.eq.ntyp1) &
!!C in UNRES uncomment the line below as GLY has no side-chain...
!C lipbufthick is thickenes of lipid buffore
sstube=sscalelip(fracinbuf)
ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
-!C print *,ssgradtube, sstube,tubetranene(itype(i))
- enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+!C print *,ssgradtube, sstube,tubetranene(itype(i,1))
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C gg_tube(3,i-1)= gg_tube(3,i-1)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C print *,"doing sccale for lower part"
elseif (positi.gt.buftubetop) then
fracinbuf=1.0d0- &
sstube=sscalelip(fracinbuf)
ssgradtube=sscagradlip(fracinbuf)/tubebufthick
- enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C gg_tube(3,i-1)= gg_tube(3,i-1)
-!C &+ssgradtube*tubetranene(itype(i))
+!C &+ssgradtube*tubetranene(itype(i,1))
!C print *, "doing sscalefor top part",sslip,fracinbuf
else
sstube=1.0d0
ssgradtube=0.0d0
- enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1))
!C print *,"I am in true lipid"
endif
else
real(kind=8) :: Etube,xtemp,xminact,yminact,&
ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,denominator,faccav,&
sc_aa_tube,sc_bb_tube,zmin,ztemp,zminact
- integer:: i,j,iti
+ integer:: i,j,iti,r
Etube=0.0d0
! print *,itube_start,itube_end,"poczatek"
!C for UNRES
do i=itube_start,itube_end
!C lets ommit dummy atoms for now
- if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+ if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle
!C now calculate distance from center of tube and direction vectors
xmin=boxxsize
ymin=boxysize
do i=itube_start,itube_end
enecavtube(i)=0.0d0
!C Lets not jump over memory as we use many times iti
- iti=itype(i)
+ iti=itype(i,1)
!C lets ommit dummy atoms for now
if ((iti.eq.ntyp1) &
!C in UNRES uncomment the line below as GLY has no side-chain...
Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) &
+enecavtube(i+nres)
enddo
+! do i=1,20
+! print *,"begin", i,"a"
+! do r=1,10000
+! rdiff=r/100.0d0
+! rdiff6=rdiff**6.0d0
+! sc_aa_tube=sc_aa_tube_par(i)
+! sc_bb_tube=sc_bb_tube_par(i)
+! enetube(i)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
+! denominator=(1.0d0+dcavtub(i)*rdiff6*rdiff6)
+! enecavtube(i)= &
+! (bcavtub(i)*rdiff+acavtub(i)*dsqrt(rdiff)+ccavtub(i)) &
+! /denominator
+
+! print '(5(f10.3,1x))',rdiff,enetube(i),enecavtube(i),enecavtube(i)+enetube(i)
+! enddo
+! print *,"end",i,"a"
+! enddo
!C print *,"ETUBE", etube
return
end subroutine calcnano
enddo
do i=ivec_start,ivec_end
!C do i=1,nres-1
-!C if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
+!C if ((itype(i,1).eq.ntyp1).and.itype(i+1,1).eq.ntyp1) cycle
ishield_list(i)=0
- if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
+ if ((itype(i,1).eq.ntyp1).and.itype(i+1,1).eq.ntyp1) cycle
!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
+ if ((itype(k,1).eq.ntyp1).or.(itype(k,1).eq.10)) cycle
dist_pep_side=0.0
dist_side_calf=0.0
do j=1,3
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))
+ short=short_r_sidechain(itype(k,1))
+ long=long_r_sidechain(itype(k,1))
costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2)
sinthet=short/dist_pep_side*costhet
!C now costhet_grad
enddo
fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
-!C write(2,*) "TOTAL VOLUME",i,itype(i),fac_shield(i)
+!C write(2,*) "TOTAL VOLUME",i,itype(i,1),fac_shield(i)
enddo
return
end subroutine set_shield_fac2
allocate(gg_tube_sc(3,-1:nres))
allocate(gg_tube(3,-1:nres))
allocate(gradafm(3,-1:nres))
+ allocate(gradb_nucl(3,-1:nres))
+ allocate(gradbx_nucl(3,-1:nres))
!(3,maxres)
allocate(grad_shield_side(3,50,nres))
allocate(grad_shield_loc(3,50,nres))
return
end subroutine alloc_ener_arrays
+!-----------------------------------------------------------------
+ subroutine ebond_nucl(estr_nucl)
+!c
+!c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds
+!c
+
+ real(kind=8),dimension(3) :: u,ud
+ real(kind=8) :: usum,uprod,uprod1,uprod2,usumsqder
+ real(kind=8) :: estr_nucl,diff
+ integer :: iti,i,j,k,nbi
+ estr_nucl=0.0d0
+!C print *,"I enter ebond"
+ if (energy_dec) &
+ write (iout,*) "ibondp_start,ibondp_end",&
+ ibondp_nucl_start,ibondp_nucl_end
+ do i=ibondp_nucl_start,ibondp_nucl_end
+ if (itype(i-1,2).eq.ntyp1_molec(2) .or. &
+ itype(i,2).eq.ntyp1_molec(2)) cycle
+! 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,vbld(i),distchainmax,
+! & gnmr1(vbld(i),-1.0d0,distchainmax)
+
+ diff = vbld(i)-vbldp0_nucl
+ if(energy_dec)write(iout,*) "estr_nucl_bb" , i,vbld(i),&
+ vbldp0_nucl,diff,AKP_nucl*diff*diff
+ estr_nucl=estr_nucl+diff*diff
+ print *,estr_nucl
+ do j=1,3
+ gradb_nucl(j,i-1)=AKP_nucl*diff*dc(j,i-1)/vbld(i)
+ enddo
+!c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
+ enddo
+ estr_nucl=0.5d0*AKP_nucl*estr_nucl
+ print *,"partial sum", estr_nucl,AKP_nucl
+
+ if (energy_dec) &
+ write (iout,*) "ibondp_start,ibondp_end",&
+ ibond_nucl_start,ibond_nucl_end
+
+ do i=ibond_nucl_start,ibond_nucl_end
+!C print *, "I am stuck",i
+ iti=itype(i,2)
+ if (iti.eq.ntyp1_molec(2)) cycle
+ nbi=nbondterm_nucl(iti)
+!C print *,iti,nbi
+ if (nbi.eq.1) then
+ diff=vbld(i+nres)-vbldsc0_nucl(1,iti)
+
+ if (energy_dec) &
+ write (iout,*) "estr_nucl_sc", i,iti,vbld(i+nres),vbldsc0_nucl(1,iti),diff, &
+ AKSC_nucl(1,iti),AKSC_nucl(1,iti)*diff*diff
+ estr_nucl=estr_nucl+0.5d0*AKSC_nucl(1,iti)*diff*diff
+ print *,estr_nucl
+ do j=1,3
+ gradbx_nucl(j,i)=AKSC_nucl(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
+ enddo
+ else
+ do j=1,nbi
+ diff=vbld(i+nres)-vbldsc0_nucl(j,iti)
+ ud(j)=aksc_nucl(j,iti)*diff
+ u(j)=abond0_nucl(j,iti)+0.5d0*ud(j)*diff
+ enddo
+ uprod=u(1)
+ do j=2,nbi
+ uprod=uprod*u(j)
+ enddo
+ usum=0.0d0
+ usumsqder=0.0d0
+ do j=1,nbi
+ uprod1=1.0d0
+ uprod2=1.0d0
+ do k=1,nbi
+ if (k.ne.j) then
+ uprod1=uprod1*u(k)
+ uprod2=uprod2*u(k)*u(k)
+ endif
+ enddo
+ usum=usum+uprod1
+ usumsqder=usumsqder+ud(j)*uprod2
+ enddo
+ estr_nucl=estr_nucl+uprod/usum
+ do j=1,3
+ gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
+ enddo
+ endif
+ enddo
+!C print *,"I am about to leave ebond"
+ return
+ end subroutine ebond_nucl
+
+!-----------------------------------------------------------------------------
+ subroutine ebend_nucl(etheta_nucl)
+ real(kind=8),dimension(nntheterm_nucl+1) :: coskt,sinkt !mmaxtheterm
+ real(kind=8),dimension(nsingle_nucl+1) :: cosph1,sinph1,cosph2,sinph2 !maxsingle
+ real(kind=8),dimension(ndouble_nucl+1,ndouble_nucl+1) :: cosph1ph2,sinph1ph2 !maxdouble,maxdouble
+ logical :: lprn=.true., lprn1=.false.
+!el local variables
+ integer :: i,k,iblock,ityp1,ityp2,ityp3,l,m
+ real(kind=8) :: dethetai,dephii,dephii1,theti2,phii,phii1,ethetai
+ real(kind=8) :: aux,etheta_nucl,ccl,ssl,scl,csl,ethetacnstr
+! local variables for constrains
+ real(kind=8) :: difi,thetiii
+ integer itheta
+ etheta_nucl=0.0D0
+ print *,"ithet_start",ithet_nucl_start," ithet_end",ithet_nucl_end,nres
+ do i=ithet_nucl_start,ithet_nucl_end
+ if ((itype(i-1,2).eq.ntyp1_molec(2)).or.&
+ (itype(i-2,2).eq.ntyp1_molec(2)).or. &
+ (itype(i,2).eq.ntyp1_molec(2))) cycle
+ dethetai=0.0d0
+ dephii=0.0d0
+ dephii1=0.0d0
+ theti2=0.5d0*theta(i)
+ ityp2=ithetyp_nucl(itype(i-1,2))
+ do k=1,nntheterm_nucl
+ coskt(k)=dcos(k*theti2)
+ sinkt(k)=dsin(k*theti2)
+ enddo
+ if (i.gt.3 .and. itype(i-2,2).ne.ntyp1_molec(2)) then
+#ifdef OSF
+ phii=phi(i)
+ if (phii.ne.phii) phii=150.0
+#else
+ phii=phi(i)
+#endif
+ ityp1=ithetyp_nucl(itype(i-2,2))
+ do k=1,nsingle_nucl
+ cosph1(k)=dcos(k*phii)
+ sinph1(k)=dsin(k*phii)
+ enddo
+ else
+ phii=0.0d0
+ ityp1=nthetyp_nucl+1
+ do k=1,nsingle_nucl
+ cosph1(k)=0.0d0
+ sinph1(k)=0.0d0
+ enddo
+ endif
+
+ if (i.lt.nres .and. itype(i,2).ne.ntyp1_molec(2)) then
+#ifdef OSF
+ phii1=phi(i+1)
+ if (phii1.ne.phii1) phii1=150.0
+ phii1=pinorm(phii1)
+#else
+ phii1=phi(i+1)
+#endif
+ ityp3=ithetyp_nucl(itype(i,2))
+ do k=1,nsingle_nucl
+ cosph2(k)=dcos(k*phii1)
+ sinph2(k)=dsin(k*phii1)
+ enddo
+ else
+ phii1=0.0d0
+ ityp3=nthetyp_nucl+1
+ do k=1,nsingle_nucl
+ cosph2(k)=0.0d0
+ sinph2(k)=0.0d0
+ enddo
+ endif
+ ethetai=aa0thet_nucl(ityp1,ityp2,ityp3)
+ do k=1,ndouble_nucl
+ do l=1,k-1
+ ccl=cosph1(l)*cosph2(k-l)
+ ssl=sinph1(l)*sinph2(k-l)
+ scl=sinph1(l)*cosph2(k-l)
+ csl=cosph1(l)*sinph2(k-l)
+ cosph1ph2(l,k)=ccl-ssl
+ cosph1ph2(k,l)=ccl+ssl
+ sinph1ph2(l,k)=scl+csl
+ sinph1ph2(k,l)=scl-csl
+ enddo
+ enddo
+ if (lprn) then
+ write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,&
+ " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
+ write (iout,*) "coskt and sinkt",nntheterm_nucl
+ do k=1,nntheterm_nucl
+ write (iout,*) k,coskt(k),sinkt(k)
+ enddo
+ endif
+ do k=1,ntheterm_nucl
+ ethetai=ethetai+aathet_nucl(k,ityp1,ityp2,ityp3)*sinkt(k)
+ dethetai=dethetai+0.5d0*k*aathet_nucl(k,ityp1,ityp2,ityp3)&
+ *coskt(k)
+ if (lprn)&
+ write (iout,*) "k",k," aathet",aathet_nucl(k,ityp1,ityp2,ityp3),&
+ " ethetai",ethetai
+ enddo
+ if (lprn) then
+ write (iout,*) "cosph and sinph"
+ do k=1,nsingle_nucl
+ write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
+ enddo
+ write (iout,*) "cosph1ph2 and sinph2ph2"
+ do k=2,ndouble_nucl
+ do l=1,k-1
+ write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),&
+ sinph1ph2(l,k),sinph1ph2(k,l)
+ enddo
+ enddo
+ write(iout,*) "ethetai",ethetai
+ endif
+ do m=1,ntheterm2_nucl
+ do k=1,nsingle_nucl
+ aux=bbthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)&
+ +ccthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k)&
+ +ddthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)&
+ +eethet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+ ethetai=ethetai+sinkt(m)*aux
+ dethetai=dethetai+0.5d0*m*aux*coskt(m)
+ dephii=dephii+k*sinkt(m)*(&
+ ccthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)-&
+ bbthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+ dephii1=dephii1+k*sinkt(m)*(&
+ eethet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)-&
+ ddthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+ if (lprn) &
+ write (iout,*) "m",m," k",k," bbthet",&
+ bbthet_nucl(k,m,ityp1,ityp2,ityp3)," ccthet",&
+ ccthet_nucl(k,m,ityp1,ityp2,ityp3)," ddthet",&
+ ddthet_nucl(k,m,ityp1,ityp2,ityp3)," eethet",&
+ eethet_nucl(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ enddo
+ enddo
+ if (lprn) &
+ write(iout,*) "ethetai",ethetai
+ do m=1,ntheterm3_nucl
+ do k=2,ndouble_nucl
+ do l=1,k-1
+ aux=ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
+ ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+&
+ ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
+ ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+ ethetai=ethetai+sinkt(m)*aux
+ dethetai=dethetai+0.5d0*m*coskt(m)*aux
+ dephii=dephii+l*sinkt(m)*(&
+ -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-&
+ ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
+ ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+&
+ ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ dephii1=dephii1+(k-l)*sinkt(m)*( &
+ -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+&
+ ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+&
+ ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-&
+ ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+ if (lprn) then
+ write (iout,*) "m",m," k",k," l",l," ffthet", &
+ ffthet_nucl(l,k,m,ityp1,ityp2,ityp3), &
+ ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ggthet",&
+ ggthet_nucl(l,k,m,ityp1,ityp2,ityp3),&
+ ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+ write (iout,*) cosph1ph2(l,k)*sinkt(m), &
+ cosph1ph2(k,l)*sinkt(m),&
+ sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
+ endif
+ enddo
+ enddo
+ enddo
+10 continue
+ if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') &
+ i,theta(i)*rad2deg,phii*rad2deg, &
+ phii1*rad2deg,ethetai
+ etheta_nucl=etheta_nucl+ethetai
+ print *,i,"partial sum",etheta_nucl
+ if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang_nucl*dephii
+ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang_nucl*dephii1
+ gloc(nphi+i-2,icg)=wang_nucl*dethetai
+ enddo
+ return
+ end subroutine ebend_nucl
+
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
end module energy
projects / unres4.git / blobdiff