!-----------------------------------------------------------------------------
! Maximum number of SC local term fitting function coefficiants
integer,parameter :: maxsccoef=65
+! Maximum number of local shielding effectors
+ integer,parameter :: maxcontsshi=50
!-----------------------------------------------------------------------------
! commom.calc common/calc/
!-----------------------------------------------------------------------------
! common /contacts/
! Change 12/1/95 - common block CONTACTS1 included.
! common /contacts1/
+
integer,dimension(:),allocatable :: num_cont !(maxres)
integer,dimension(:,:),allocatable :: jcont !(maxconts,maxres)
- real(kind=8),dimension(:,:),allocatable :: facont !(maxconts,maxres)
+ real(kind=8),dimension(:,:),allocatable :: facont,ees0plist !(maxconts,maxres)
real(kind=8),dimension(:,:,:),allocatable :: gacont !(3,maxconts,maxres)
+ integer,dimension(:),allocatable :: ishield_list
+ integer,dimension(:,:),allocatable :: shield_list
!
! 12/26/95 - H-bonding contacts
! common /contacts_hb/
real(kind=8),dimension(:,:),allocatable :: gvdwc,gelc,gelc_long,&
gvdwpp,gvdwc_scpp,gradx_scp,gvdwc_scp,ghpbx,ghpbc,&
gradcorr,gradcorr_long,gradcorr5_long,gradcorr6_long,&
- gcorr6_turn_long,gradxorr,gradcorr5,gradcorr6 !(3,maxres)
+ gcorr6_turn_long,gradxorr,gradcorr5,gradcorr6,gliptran,gliptranc,&
+ gliptranx, &
+ gshieldx,gshieldc,gshieldc_loc,gshieldx_ec,&
+ gshieldc_ec,gshieldc_loc_ec,gshieldx_t3, &
+ gshieldc_t3,gshieldc_loc_t3,gshieldx_t4,gshieldc_t4, &
+ gshieldc_loc_t4,gshieldx_ll,gshieldc_ll,gshieldc_loc_ll,&
+ grad_shield !(3,maxres)
! 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),dimension(:,:,:),allocatable :: dtheta !(3,2,maxres)
real(kind=8),dimension(:,:),allocatable :: gscloc,gsclocx !(3,maxres)
! real(kind=8),dimension(:,:,:),allocatable :: dphi,dalpha,domega !(3,3,maxres)
+ real(kind=8),dimension(:,:,:),allocatable :: grad_shield_side, &
+ grad_shield_loc ! (3,maxcontsshileding,maxnres)
! integer :: nfl,icg
! common /deriv_loc/
+ real(kind=8), dimension(:),allocatable :: fac_shield
real(kind=8),dimension(3,5,2) :: derx,derx_turn
! common /deriv_scloc/
real(kind=8),dimension(:,:),allocatable :: dXX_C1tab,dYY_C1tab,&
integer :: n_corr,n_corr1,ierror
real(kind=8) :: etors,edihcnstr,etors_d,esccor,ehpb
real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,escloc,ees,eel_loc
- real(kind=8) :: eello_turn3,eello_turn4,estr,ebe
+ real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran
real(kind=8) :: ecorr,ecorr5,ecorr6,eturn6
#ifdef MPI
#endif
!
! Compute the side-chain and electrostatic interaction energy
-!
+ print *, "Before EVDW"
! goto (101,102,103,104,105,106) ipot
select case(ipot)
! Lennard-Jones potential.
! 50 continue
end select
! continue
-
+! print *,"after EGB"
+! shielding effect
+ if (shield_mode.eq.2) then
+ call set_shield_fac2
+ endif
!mc
!mc Sep-06: egb takes care of dynamic ss bonds too
!mc
#ifdef TIMING
time_vec=time_vec+MPI_Wtime()-time01
#endif
-! print *,"Processor",myrank," left VEC_AND_DERIV"
+! print *,"Processor",myrank," left VEC_AND_DERIV"
if (ipot.lt.6) then
#ifdef SPLITELE
+ print *,"after ipot if", ipot
if (welec.gt.0d0.or.wvdwpp.gt.0d0.or.wel_loc.gt.0d0.or. &
wturn3.gt.0d0.or.wturn4.gt.0d0 .or. wcorr.gt.0.0d0 &
.or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.d0 &
.or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.d0 &
.or. wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0 ) then
#endif
+! print *,"just befor eelec call"
call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
-! write (iout,*) "ELEC calc"
+! write (iout,*) "ELEC calc"
else
ees=0.0d0
evdw1=0.0d0
! write (iout,*) "Soft-sphere SCP potential"
call escp_soft_sphere(evdw2,evdw2_14)
endif
-!elwrite(iout,*) "in etotal before ebond",ipot
+! write(iout,*) "in etotal before ebond",ipot
!
! Calculate the bond-stretching energy
!
call ebond(estr)
-!elwrite(iout,*) "in etotal afer ebond",ipot
+! write(iout,*) "in etotal afer ebond",ipot
!
! Calculate the disulfide-bridge and other energy and the contributions
Uconst=0.0d0
Uconst_back=0.0d0
endif
-!elwrite(iout,*) "after Econstr"
+ call flush(iout)
+! write(iout,*) "after Econstr"
+
+ if (wliptran.gt.0) then
+! print *,"PRZED WYWOLANIEM"
+ call Eliptransfer(eliptran)
+ else
+ eliptran=0.0d0
+ endif
#ifdef TIMING
time_enecalc=time_enecalc+MPI_Wtime()-time00
energia(17)=estr
energia(20)=Uconst+Uconst_back
energia(21)=esccor
+ energia(22)=eliptran
! 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"
logical :: reduce
real(kind=8) :: evdw,evdw2,evdw2_14,ees,evdw1,ecorr,ecorr5,ecorr6
real(kind=8) :: eel_loc,eello_turn3,eello_turn4,eturn6,ebe,escloc
- real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,esccor,etot
+ real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,esccor,etot, &
+ eliptran
integer :: i
#ifdef MPI
integer :: ierr
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ eliptran=energia(22)
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 &
+wang*ebe+wtor*etors+wscloc*escloc &
+wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
- +wbond*estr+Uconst+wsccor*esccor
+ +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
+wang*ebe+wtor*etors+wscloc*escloc &
+wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
- +wbond*estr+Uconst+wsccor*esccor
+ +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
#endif
energia(0)=etot
! detecting NaNQ
!el local variables
real(kind=8) :: etot,evdw,evdw2,ees,evdw1,ecorr,ecorr5,ecorr6,eel_loc
real(kind=8) :: eello_turn6,eello_turn3,eello_turn4,ebe,escloc
- real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor
+ real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran
etot=energia(0)
evdw=energia(1)
estr=energia(17)
Uconst=energia(20)
esccor=energia(21)
+ eliptran=energia(22)
+
#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,ebr*nss,&
- Uconst,etot
+ Uconst,eliptran,wliptran,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ &
'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ &
'UCONST= ',1pE16.6,' (Constraint energy)'/ &
+ 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/&
'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
ecorr,wcorr,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,&
- ebr*nss,Uconst,etot
+ ebr*nss,Uconst,eliptran,wliptran,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ &
'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ &
'UCONST=',1pE16.6,' (Constraint energy)'/ &
+ 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ &
'ETOT= ',1pE16.6,' (total)')
#endif
return
! include 'COMMON.NAMES'
! include 'COMMON.IOUNITS'
! include 'COMMON.CONTACTS'
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
integer :: num_conti
!el local variables
integer :: i,itypi,iint,j,itypi1,itypj,k
! 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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e1+e2
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
logical :: scheck
!el local variables
integer :: i,iint,j,itypi,itypi1,k,itypj
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e_augm+e1+e2
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
! Calculate whole angle-dependent part of epsilon and contributions
! to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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 & epsi,sigm,chi1,chi2,chip1,chip2,
real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi
real(kind=8) :: evdw,sig0ij
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
- dist_temp, dist_init
+ dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, &
+ sslipi,sslipj,faclip
integer :: ii
+ real(kind=8) :: fracinbuf
+
!cccc energy_dec=.false.
! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
! if (icall.eq.0) lprn=.false.
!el ind=0
do i=iatsc_s,iatsc_e
+ print *,"I am in EVDW",i
itypi=iabs(itype(i))
if (itypi.eq.ntyp1) cycle
itypi1=iabs(itype(i+1))
zi=dmod(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
+ print *, sslipi,ssgradlipi
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
if (yj.lt.0) yj=yj+boxysize
zj=dmod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+! print *,"tu",xi,yi,zi,xj,yj,zj
+! print *,"tu2",j,j+nres,c(1,j),c(1,j+nres)
+! this fragment set correct epsilon for lipid phase
+ 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
+!------------------------------------------------
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
!---------------------------------------------------------------
rij_shift=1.0D0/rij_shift
fac=rij_shift**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ faclip=fac
+ e1=fac*fac*aa!(itypi,itypj)
+ e2=fac*bb!(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*sss_ele_cut
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa!(itypi,itypj)
write (iout,'(2(a3,i3,2x),17(0pf7.3))') &
restyp(itypi),i,restyp(itypj),j, &
epsi,sigm,chi1,chi2,chip1,chip2, &
evdwij
endif
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
- 'evdw',i,j,evdwij !,"egb"
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2e10.2,e11.3)')&
+ 'evdw',i,j,evdwij,xi,xj,rij !,"egb"
+!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
gg(1)=xj*fac
gg(2)=yj*fac
gg(3)=zj*fac
+!C Calculate the radial part of the gradient
+ gg_lipi(3)=eps1*(eps2rt*eps2rt)&
+ *(eps3rt*eps3rt)*sss_ele_cut/2.0d0*(faclip*faclip*&
+ (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))&
+ +faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
+ gg_lipj(3)=ssgradlipj*gg_lipi(3)
+ gg_lipi(3)=gg_lipi(3)*ssgradlipi
+
! print *,'before sc_grad', gg(1),gg(2),gg(3)
! Calculate angular part of the gradient.
call sc_grad
!---------------------------------------------------------------
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij+e_augm
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
! include 'COMMON.NAMES'
! include 'COMMON.IOUNITS'
! include 'COMMON.CONTACTS'
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
!d print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
!el local variables
integer :: i,iint,j,itypi,itypi1,itypj,k
real(kind=8) :: auxvec(2),auxmat(2,2)
integer :: i,iti1,iti,k,l
real(kind=8) :: sin1,cos1,sin2,cos2,dwacos2,dwasin2
-
+! print *,"in set matrices"
!
! Compute the virtual-bond-torsional-angle dependent quantities needed
! to calculate the el-loc multibody terms of various order.
#else
do i=3,nres+1
#endif
+! print *,i,"i"
if (i .lt. nres+1) then
sin1=dsin(phi(i))
cos1=dcos(phi(i))
else
iti1=ntortyp+1
endif
+! print *,iti,i,"iti",iti1,itype(i-1),itype(i-2)
!d write (iout,*) '*******i',i,' iti1',iti
!d write (iout,*) 'b1',b1(:,iti)
!d write (iout,*) 'b2',b2(:,iti)
!el local variables
integer :: i,k,j
real(kind=8) :: ees,evdw1,eel_loc,eello_turn3,eello_turn4
- real(kind=8) :: fac,t_eelecij
+ real(kind=8) :: fac,t_eelecij,fracinbuf
!d write(iout,*) 'In EELEC'
+ print *,"IN EELEC"
!d do i=1,nloctyp
!d write(iout,*) 'Type',i
!d write(iout,*) 'B1',B1(:,i)
! write (iout,*) 'i',i,' fac',fac
enddo
endif
+ print *,wel_loc,"wel_loc",wcorr4,wcorr5,wcorr6,wturn3,wturn4, &
+ wturn6
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
#ifdef TIMING
time01=MPI_Wtime()
#endif
+! print *, "before set matrices"
call set_matrices
+! print *, "after set matrices"
+
#ifdef TIMING
time_mat=time_mat+MPI_Wtime()-time01
#endif
endif
+ print *, "after set matrices"
!d do i=1,nres-1
!d write (iout,*) 'i=',i
!d do k=1,3
!
-
+ 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
zmedi=dmod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
num_conti=0
- call eelecij(i,i+2,ees,evdw1,eel_loc)
+ if ((zmedi.gt.bordlipbot) &
+ .and.(zmedi.lt.bordliptop)) then
+!C the energy transfer exist
+ if (zmedi.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((zmedi-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+ print *,i,sslipi,ssgradlipi
+ 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
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=dmod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ if ((zmedi.gt.bordlipbot) &
+ .and.(zmedi.lt.bordliptop)) then
+!C the energy transfer exist
+ if (zmedi.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((zmedi-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+
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 (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=dmod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ if ((zmedi.gt.bordlipbot) &
+ .and.(zmedi.lt.bordliptop)) then
+!C the energy transfer exist
+ if (zmedi.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((zmedi-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
num_conti=num_cont_hb(i)
!el real(kind=8),dimension(3,4) :: agg,aggi,aggi1,aggj,aggj1
real(kind=8),dimension(4) :: muij
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
- dist_temp, dist_init
- integer xshift,yshift,zshift
+ dist_temp, dist_init,rlocshield,fracinbuf
+ integer xshift,yshift,zshift,ilist,iresshield
!el integer :: num_conti,j1,j2
!el real(kind=8) :: a22,a23,a32,a33,dxi,dyi,dzi,dx_normi,dy_normi,&
!el dz_normi,xmedi,ymedi,zmedi
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
+
isubchap=0
dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
xj_safe=xj
evdwij=ev1+ev2
el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
el2=fac4*fac
- eesij=el1+el2
+! eesij=el1+el2
+ 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*sss_ele_cut
+!C FOR NOW SHIELD IS NOT USED WITH LIPSCALE
+!C & *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ else
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+ eesij=(el1+el2)
+ ees=ees+eesij &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)*sss_ele_cut
+!C print *,"TUCC",(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+ endif
+
! 12/26/95 - for the evaluation of multi-body H-bonding interactions
ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
- ees=ees+eesij*sss_ele_cut
- evdw1=evdw1+evdwij*sss_ele_cut
+! ees=ees+eesij*sss_ele_cut
+ evdw1=evdw1+evdwij*sss_ele_cut &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
!d write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
!d & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
!d & 1.0D0/dsqrt(rrmij),evdwij,eesij,
! Calculate contributions to the Cartesian gradient.
!
#ifdef SPLITELE
- facvdw=-6*rrmij*(ev1+evdwij)*sss_ele_cut
- facel=-3*rrmij*(el1+eesij)*sss_ele_cut
+ facvdw=-6*rrmij*(ev1+evdwij)*sss_ele_cut &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ facel=-3*rrmij*(el1+eesij)*sss_ele_cut &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
fac1=fac
erij(1)=xj*rmij
erij(2)=yj*rmij
ggg(2)=facel*yj+sss_ele_grad*rmij*eesij*yj
ggg(3)=facel*zj+sss_ele_grad*rmij*eesij*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*sss_ele_cut
+ gshieldx(k,iresshield)=gshieldx(k,iresshield)+ &
+ rlocshield &
+ +grad_shield_loc(k,ilist,i)*eesij/fac_shield(i)*2.0 &
+ *sss_ele_cut
+ gshieldc(k,iresshield-1)=gshieldc(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)*eesij/fac_shield(j) &
+ *2.0*sss_ele_cut
+ gshieldx(k,iresshield)=gshieldx(k,iresshield)+ &
+ rlocshield &
+ +grad_shield_loc(k,ilist,j)*eesij/fac_shield(j)*2.0 &
+ *sss_ele_cut
+ gshieldc(k,iresshield-1)=gshieldc(k,iresshield-1)+rlocshield
+ enddo
+ enddo
+ do k=1,3
+ gshieldc(k,i)=gshieldc(k,i)+ &
+ grad_shield(k,i)*eesij/fac_shield(i)*2.0 &
+ *sss_ele_cut
+
+ gshieldc(k,j)=gshieldc(k,j)+ &
+ grad_shield(k,j)*eesij/fac_shield(j)*2.0 &
+ *sss_ele_cut
+
+ gshieldc(k,i-1)=gshieldc(k,i-1)+ &
+ grad_shield(k,i)*eesij/fac_shield(i)*2.0 &
+ *sss_ele_cut
+
+ gshieldc(k,j-1)=gshieldc(k,j-1)+ &
+ grad_shield(k,j)*eesij/fac_shield(j)*2.0 &
+ *sss_ele_cut
+
+ enddo
+ endif
+
+
! do k=1,3
! ghalf=0.5D0*ggg(k)
! gelc(k,i)=gelc(k,i)+ghalf
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
enddo
+ gelc_long(3,j)=gelc_long(3,j)+ &
+ ssgradlipj*eesij/2.0d0*lipscale**2&
+ *sss_ele_cut
+
+ gelc_long(3,i)=gelc_long(3,i)+ &
+ ssgradlipi*eesij/2.0d0*lipscale**2&
+ *sss_ele_cut
+
+
!
! Loop over residues i+1 thru j-1.
!
!grad gelc(l,k)=gelc(l,k)+ggg(l)
!grad enddo
!grad enddo
- ggg(1)=facvdw*xj+sss_ele_grad*rmij*evdwij*xj
- ggg(2)=facvdw*yj+sss_ele_grad*rmij*evdwij*yj
- ggg(3)=facvdw*zj+sss_ele_grad*rmij*evdwij*zj
+ ggg(1)=facvdw*xj+sss_ele_grad*rmij*evdwij*xj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ ggg(2)=facvdw*yj+sss_ele_grad*rmij*evdwij*yj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ ggg(3)=facvdw*zj+sss_ele_grad*rmij*evdwij*zj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
! do k=1,3
! ghalf=0.5D0*ggg(k)
! gvdwpp(k,i)=gvdwpp(k,i)+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.
+
+!C Lipidic part for scaling weight
+ gvdwpp(3,j)=gvdwpp(3,j)+ &
+ sss_ele_cut*ssgradlipj*evdwij/2.0d0*lipscale**2
+ gvdwpp(3,i)=gvdwpp(3,i)+ &
+ sss_ele_cut*ssgradlipi*evdwij/2.0d0*lipscale**2
+!! Loop over residues i+1 thru j-1.
!
!grad do k=i+1,j-1
!grad do l=1,3
!grad enddo
!grad enddo
#else
- facvdw=(ev1+evdwij)*sss_ele_cut
+ facvdw=(ev1+evdwij)*sss_ele_cut &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
facel=(el1+eesij)*sss_ele_cut
fac1=fac
fac=-3*rrmij*(facvdw+facvdw+facel)
!grad enddo
!grad enddo
! 9/28/08 AL Gradient compotents will be summed only at the end
- ggg(1)=facvdw*xj
- ggg(2)=facvdw*yj
- ggg(3)=facvdw*zj
+ ggg(1)=facvdw*xj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ ggg(2)=facvdw*yj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ ggg(3)=facvdw*zj &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
do k=1,3
gvdwpp(k,j)=gvdwpp(k,j)+ggg(k)
gvdwpp(k,i)=gvdwpp(k,i)-ggg(k)
enddo
+ gvdwpp(3,j)=gvdwpp(3,j)+ &
+ sss_ele_cut*ssgradlipj*evdwij/2.0d0*lipscale**2
+ gvdwpp(3,i)=gvdwpp(3,i)+ &
+ sss_ele_cut*ssgradlipi*evdwij/2.0d0*lipscale**2
+
#endif
!
! Angular part
!d print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
!d & (dcosg(k),k=1,3)
do k=1,3
- ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*sss_ele_cut
+ ggg(k)=(ecosb*dcosb(k)+ecosg*dcosg(k))*sss_ele_cut &
+ *fac_shield(i)**2*fac_shield(j)**2 &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
enddo
! do k=1,3
! ghalf=0.5D0*ggg(k)
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)&
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)**2*fac_shield(j)**2 &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
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)&
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)**2*fac_shield(j)**2 &
+ *((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
gelc_long(k,j)=gelc_long(k,j)+ggg(k)
gelc_long(k,i)=gelc_long(k,i)-ggg(k)
enddo
! Contribution to the local-electrostatic energy coming from the i-j pair
eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3) &
+a33*muij(4)
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+ endif
+ eel_loc_ij=eel_loc_ij &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+!C Now derivative over eel_loc
+ if ((fac_shield(i).gt.0).and.(fac_shield(j).gt.0).and. &
+ (shield_mode.gt.0)) then
+!C print *,i,j
+
+ do ilist=1,ishield_list(i)
+ iresshield=shield_list(ilist,i)
+ do k=1,3
+ rlocshield=grad_shield_side(k,ilist,i)*eel_loc_ij &
+ /fac_shield(i)&
+ *sss_ele_cut
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ &
+ rlocshield &
+ +grad_shield_loc(k,ilist,i)*eel_loc_ij/fac_shield(i) &
+ *sss_ele_cut
+
+ 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) &
+ *sss_ele_cut
+ gshieldx_ll(k,iresshield)=gshieldx_ll(k,iresshield)+ &
+ rlocshield &
+ +grad_shield_loc(k,ilist,j)*eel_loc_ij/fac_shield(j) &
+ *sss_ele_cut
+
+ 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) &
+ *sss_ele_cut
+ gshieldc_ll(k,j)=gshieldc_ll(k,j)+ &
+ grad_shield(k,j)*eel_loc_ij/fac_shield(j) &
+ *sss_ele_cut
+ gshieldc_ll(k,i-1)=gshieldc_ll(k,i-1)+ &
+ grad_shield(k,i)*eel_loc_ij/fac_shield(i) &
+ *sss_ele_cut
+ gshieldc_ll(k,j-1)=gshieldc_ll(k,j-1)+ &
+ grad_shield(k,j)*eel_loc_ij/fac_shield(j) &
+ *sss_ele_cut
+
+ enddo
+ endif
+
+
! write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
! eel_loc_ij=0.0
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
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)) &
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
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)) &
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
! Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
! do l=1,3
! ggg(1)=(agg(1,1)*muij(1)+ &
!grad gel_loc(l,i)=gel_loc(l,i)+ghalf
!grad gel_loc(l,j)=gel_loc(l,j)+ghalf
enddo
+ gel_loc_long(3,j)=gel_loc_long(3,j)+ &
+ ssgradlipj*eel_loc_ij/2.0d0*lipscale/ &
+ ((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+ gel_loc_long(3,i)=gel_loc_long(3,i)+ &
+ ssgradlipi*eel_loc_ij/2.0d0*lipscale/ &
+ ((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
!grad do k=i+1,j2
!grad do l=1,3
!grad gel_loc(l,k)=gel_loc(l,k)+ggg(l)
else
ees0pij=0
endif
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0d0
+ fac_shield(j)=1.0d0
+ else
+ ees0plist(num_conti,i)=j
+ endif
! 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
endif
! ees0mij=0.0D0
ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) &
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)*fac_shield(j)
ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) &
- *sss_ele_cut
+ *sss_ele_cut &
+ *fac_shield(i)*fac_shield(j)
! Diagnostics. Comment out or remove after debugging!
! ees0p(num_conti,i)=0.5D0*fac3*ees0pij
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) &
- *sss_ele_cut
+ *sss_ele_cut*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)&
- *sss_ele_cut
+ *sss_ele_cut*fac_shield(i)*fac_shield(j)
gacontp_hb3(k,num_conti,i)=gggp(k) &
- *sss_ele_cut
+ *sss_ele_cut*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) &
- *sss_ele_cut
+ *sss_ele_cut*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) &
- *sss_ele_cut
+ *sss_ele_cut*fac_shield(i)*fac_shield(j)
gacontm_hb3(k,num_conti,i)=gggm(k) &
- *sss_ele_cut
+ *sss_ele_cut*fac_shield(i)*fac_shield(j)
enddo
! Diagnostics. Comment out or remove after debugging!
!el dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
!el num_conti,j1,j2
!el local variables
- integer :: i,j,l
- real(kind=8) :: eello_turn3
+ integer :: i,j,l,k,ilist,iresshield
+ real(kind=8) :: eello_turn3,zj,fracinbuf,eello_t3, rlocshield
j=i+2
! write (iout,*) "eturn3",i,j,j1,j2
+ zj=(c(3,j)+c(3,j+1))/2.0d0
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.lt.0)) write (*,*) "CHUJ"
+ 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
+
a_temp(1,1)=a22
a_temp(1,2)=a23
a_temp(2,1)=a32
call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
call transpose2(auxmat(1,1),auxmat1(1,1))
call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
- eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0d0
+ fac_shield(j)=1.0d0
+ endif
+
+ eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+ eello_t3= &
+ 0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j)
+
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
'eturn3',i,j,0.5d0*(pizda(1,1)+pizda(2,2))
+ 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)
+ 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)
+ 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
+
!d write (2,*) 'i,',i,' j',j,'eello_turn3',
!d & 0.5d0*(pizda(1,1)+pizda(2,2)),
!d & ' eello_turn3_num',4*eello_turn3_num
call transpose2(auxmat2(1,1),auxmat3(1,1))
call matmat2(a_temp(1,1),auxmat3(1,1),pizda(1,1))
gel_loc_turn3(i+1)=gel_loc_turn3(i+1) &
- +0.5d0*(pizda(1,1)+pizda(2,2))
+ +0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
! Cartesian derivatives
do l=1,3
! ghalf1=0.5d0*agg(l,1)
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))
+ +0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
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))
+ +0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
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))
+ +0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
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(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))
+ +0.5d0*(pizda(1,1)+pizda(2,2)) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
+ gshieldc_t3(3,i)=gshieldc_t3(3,i)+ &
+ ssgradlipi*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,j)=gshieldc_t3(3,j)+ &
+ ssgradlipj*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,i-1)=gshieldc_t3(3,i-1)+ &
+ ssgradlipi*eello_t3/4.0d0*lipscale
+ gshieldc_t3(3,j-1)=gshieldc_t3(3,j-1)+ &
+ ssgradlipj*eello_t3/4.0d0*lipscale
+
return
end subroutine eturn3
!-----------------------------------------------------------------------------
!el dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,&
!el num_conti,j1,j2
!el local variables
- integer :: i,j,iti1,iti2,iti3,l
- real(kind=8) :: eello_turn4,s1,s2,s3
+ integer :: i,j,iti1,iti2,iti3,l,k,ilist,iresshield
+ real(kind=8) :: eello_turn4,s1,s2,s3,zj,fracinbuf,eello_t4,&
+ rlocshield
j=i+3
!CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
!CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
!d call checkint_turn4(i,a_temp,eello_turn4_num)
! write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2
+ zj=(c(3,j)+c(3,j+1))/2.0d0
+ 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
+
a_temp(1,1)=a22
a_temp(1,2)=a23
a_temp(2,1)=a32
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))
- eello_turn4=eello_turn4-(s1+s2+s3)
+ if (shield_mode.eq.0) then
+ fac_shield(i)=1.0
+ fac_shield(j)=1.0
+ endif
+
+ eello_turn4=eello_turn4-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+ eello_t4=-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j)
+!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)
+ 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)
+ 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
+
if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') &
'eturn4',i,j,-(s1+s2+s3)
!d write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
s1=scalar2(b1(1,iti2),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)
+ gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
! Derivatives in gamma(i+1)
call transpose2(EUgder(1,1,i+2),e2tder(1,1))
call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
call matmat2(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)
+ gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
! Derivatives in gamma(i+2)
call transpose2(EUgder(1,1,i+3),e3tder(1,1))
call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
call matmat2(auxmat(1,1),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)
+ gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
! Cartesian derivatives
! Derivatives of this turn contributions in DC(i+2)
if (j.lt.nres-1) then
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)
+ gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
a_temp(2,1)=aggi1(l,3)
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)
+ gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
a_temp(2,1)=aggj(l,3)
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)
+ gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
+
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
a_temp(2,1)=aggj1(l,3)
call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
! 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)
+ gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) &
+ *fac_shield(i)*fac_shield(j) &
+ *((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
enddo
+ gshieldc_t4(3,i)=gshieldc_t4(3,i)+ &
+ ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j)=gshieldc_t4(3,j)+ &
+ ssgradlipj*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,i-1)=gshieldc_t4(3,i-1)+ &
+ ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j-1)=gshieldc_t4(3,j-1)+ &
+ ssgradlipj*eello_t4/4.0d0*lipscale
+
return
end subroutine eturn4
!-----------------------------------------------------------------------------
real(kind=8),dimension(3) :: gx,gx1
logical :: lprn
!el local variables
- integer :: i,j,k,l,jj,kk,ll
+ integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield
real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,&
ees0mkl,ees,coeffpees0pij,coeffmees0mij,&
- coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl
+ coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, &
+ rlocshield
lprn=.false.
eij=facont_hb(jj,i)
!grad enddo
! write (iout,*) "ehbcorr",ekont*ees
ehbcorr=ekont*ees
+ 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)
+ 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)
+ 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)
+ 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)
+ 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
+ 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 function ehbcorr
#ifdef MOMENT
#ifdef MPI
include 'mpif.h'
#endif
- real(kind=8),dimension(3,nres) :: gradbufc,gradbufx,gradbufc_sum,&
+ real(kind=8),dimension(3,-1:nres) :: gradbufc,gradbufx,gradbufc_sum,&
gloc_scbuf !(3,maxres)
real(kind=8),dimension(4*nres) :: glocbuf !(4*maxres)
call flush(iout)
#endif
#ifdef SPLITELE
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+ &
wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+ &
wcorr5*gradcorr5_long(j,i)+ &
wcorr6*gradcorr6_long(j,i)+ &
wturn6*gcorr6_turn_long(j,i)+ &
- wstrain*ghpbc(j,i)
+ wstrain*ghpbc(j,i) &
+ +wliptran*gliptranc(j,i) &
+ +welec*gshieldc(j,i) &
+ +wcorr*gshieldc_ec(j,i) &
+ +wturn3*gshieldc_t3(j,i)&
+ +wturn4*gshieldc_t4(j,i)&
+ +wel_loc*gshieldc_ll(j,i)
+
+
enddo
enddo
#else
- do i=1,nct
+ do i=0,nct
do j=1,3
gradbufc(j,i)=wsc*gvdwc(j,i)+ &
wscp*(gvdwc_scp(j,i)+gvdwc_scpp(j,i))+ &
wcorr5*gradcorr5_long(j,i)+ &
wcorr6*gradcorr6_long(j,i)+ &
wturn6*gcorr6_turn_long(j,i)+ &
- wstrain*ghpbc(j,i)
+ wstrain*ghpbc(j,i) &
+ +wliptran*gliptranc(j,i) &
+ +welec*gshieldc(j,i)&
+ +wcorr*gshieldc_ec(j,i) &
+ +wturn4*gshieldc_t4(j,i) &
+ +wel_loc*gshieldc_ll(j,i)
+
+
enddo
enddo
#endif
enddo
call flush(iout)
#endif
- do i=1,nres
+ do i=0,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
enddo
#ifdef TIMING
! time_allreduce=time_allreduce+MPI_Wtime()-time00
#endif
- do i=nnt,nres
+ do i=0,nres
do k=1,3
gradbufc(k,i)=0.0d0
enddo
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
call flush(iout)
#endif
!el#undef DEBUG
- do i=1,nres
+ do i=-1,nres
do j=1,3
gradbufc_sum(j,i)=gradbufc(j,i)
gradbufc(j,i)=0.0d0
do j=1,3
gradbufc(j,nres-1)=gradbufc_sum(j,nres)
enddo
- do i=nres-2,nnt,-1
+ do i=nres-2,-1,-1
do j=1,3
gradbufc(j,i)=gradbufc(j,i+1)+gradbufc_sum(j,i+1)
enddo
!el if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2)
!el if (.not.allocated(gradc)) allocate(gradc(3,nres,2)) !(3,maxres,2)
!el-----------------
- do i=1,nct
+ do i=-1,nct
do j=1,3
#ifdef SPLITELE
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ &
wcorr6*gradcorr6(j,i)+ &
wturn6*gcorr6_turn(j,i)+ &
wsccor*gsccorc(j,i) &
- +wscloc*gscloc(j,i)
+ +wscloc*gscloc(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)
+
#else
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ &
wel_loc*gel_loc(j,i)+ &
wcorr6*gradcorr6(j,i)+ &
wturn6*gcorr6_turn(j,i)+ &
wsccor*gsccorc(j,i) &
- +wscloc*gscloc(j,i)
+ +wscloc*gscloc(j,i) &
+ +wliptran*gliptranc(j,i) &
+ +welec*gshieldc(j,i) &
+ +welec*gshieldc_loc(j,) &
+ +wcorr*gshieldc_ec(j,i) &
+ +wcorr*gshieldc_loc_ec(j,i) &
+ +wturn3*gshieldc_t3(j,i) &
+ +wturn3*gshieldc_loc_t3(j,i) &
+ +wturn4*gshieldc_t4(j,i) &
+ +wturn4*gshieldc_loc_t4(j,i) &
+ +wel_loc*gshieldc_ll(j,i) &
+ +wel_loc*gshieldc_loc_ll(j,i)
+
+
#endif
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ &
wbond*gradbx(j,i)+ &
wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ &
wsccor*gsccorx(j,i) &
- +wscloc*gsclocx(j,i)
+ +wscloc*gsclocx(j,i) &
+ +wliptran*gliptranx(j,i) &
+ +welec*gshieldx(j,i) &
+ +wcorr*gshieldx_ec(j,i) &
+ +wturn3*gshieldx_t3(j,i) &
+ +wturn4*gshieldx_t4(j,i) &
+ +wel_loc*gshieldx_ll(j,i)
+
enddo
enddo
#ifdef DEBUG
enddo
! write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
- gvdwx(k,i)=gvdwx(k,i)-gg(k) &
+ gvdwx(k,i)=gvdwx(k,i)-gg(k) +gg_lipi(k)&
+(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
+eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv &
*sss_ele_cut
- gvdwx(k,j)=gvdwx(k,j)+gg(k) &
+ gvdwx(k,j)=gvdwx(k,j)+gg(k)+gg_lipj(k)&
+(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv &
*sss_ele_cut
!grad enddo
!grad enddo
do l=1,3
- gvdwc(l,i)=gvdwc(l,i)-gg(l)
- gvdwc(l,j)=gvdwc(l,j)+gg(l)
+ gvdwc(l,i)=gvdwc(l,i)-gg(l)+gg_lipi(l)
+ gvdwc(l,j)=gvdwc(l,j)+gg(l)+gg_lipj(l)
enddo
return
end subroutine sc_grad
endif
return
end function sscagrad_ele
+ real(kind=8) function sscalelip(r)
+ real(kind=8) r,gamm
+ sscalelip=1.0d0+r*r*(2.0d0*r-3.0d0)
+ return
+ end function sscalelip
+!C-----------------------------------------------------------------------
+ real(kind=8) function sscagradlip(r)
+ real(kind=8) r,gamm
+ sscagradlip=r*(6.0d0*r-6.0d0)
+ return
+ end function sscagradlip
+
!!!!!!!!!!!!!!!
!-----------------------------------------------------------------------------
subroutine elj_long(evdw)
! include 'COMMON.IOUNITS'
! include 'COMMON.CONTACTS'
real(kind=8),parameter :: accur=1.0d-10
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
!el local variables
integer :: i,iint,j,k,itypi,itypi1,itypj
real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
rrij=1.0D0/rij
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e1+e2
evdw=evdw+(1.0d0-sss)*evdwij
!
! include 'COMMON.IOUNITS'
! include 'COMMON.CONTACTS'
real(kind=8),parameter :: accur=1.0d-10
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
!el local variables
integer :: i,iint,j,k,itypi,itypi1,itypj,num_conti
real(kind=8) :: xi,yi,zi,xj,yj,zj,rij,sss,rrij,fac,eps0ij
rrij=1.0D0/rij
eps0ij=eps(itypi,itypj)
fac=rrij**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e1+e2
evdw=evdw+sss*evdwij
!
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
logical :: scheck
!el local variables
integer :: i,iint,j,k,itypi,itypi1,itypj
if (sss.lt.1.0d0) then
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e_augm+e1+e2
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- real(kind=8),dimension(3) :: gg
+ real(kind=8),dimension(3) :: gg,gg_lipi,gg_lipj
logical :: scheck
!el local variables
integer :: i,iint,j,k,itypi,itypi1,itypj
if (sss.gt.0.0d0) then
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=e_augm+e1+e2
!d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
!d epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
! Calculate whole angle-dependent part of epsilon and contributions
! to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*(1.0d0-sss)
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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 & epsi,sigm,chi1,chi2,chip1,chip2,
! Calculate whole angle-dependent part of epsilon and contributions
! to its derivatives
fac=(rrij*sigsq)**expon2
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+evdwij*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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 & epsi,sigm,chi1,chi2,chip1,chip2,
real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,sig,sig0ij,rij_shift
real(kind=8) :: sss,e1,e2,evdw,sss_grad
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
- dist_temp, dist_init
+ dist_temp, dist_init,aa,bb,fracinbuf,sslipi,sslipj,&
+ ssgradlipi,ssgradlipj
+
evdw=0.0D0
!cccc energy_dec=.false.
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)
!
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)') &
+ 'evdw',i,j,evdwij,' ss'
+! if (energy_dec) write (iout,*) &
+! 'evdw',i,j,evdwij,' ss'
+ ELSE
!el ind=ind+1
itypj=itype(j)
if (itypj.eq.ntyp1) cycle
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot) &
+ .and.(zj.lt.bordliptop)) then
+!C the energy transfer exist
+ if (zj.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((zj-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+ +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+ +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
!---------------------------------------------------------------
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
evdw=evdw+evdwij*(1.0d0-sss)*sss_ele_cut
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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,&
epsi,sigm,chi1,chi2,chip1,chip2,&
gg(3)=zj*fac
! Calculate angular part of the gradient.
call sc_grad_scale(1.0d0-sss)
+ ENDIF !mask_dyn_ss
endif
enddo ! j
enddo ! iint
real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,sig0ij,sig
real(kind=8) :: sss,e1,e2,evdw,rij_shift,sss_grad
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
- dist_temp, dist_init
+ dist_temp, dist_init,aa,bb,fracinbuf,sslipi,sslipj,&
+ ssgradlipi,ssgradlipj
evdw=0.0D0
!cccc energy_dec=.false.
! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
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)
!
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)') &
+ 'evdw',i,j,evdwij,' ss'
+! if (energy_dec) write (iout,*) &
+! 'evdw',i,j,evdwij,' ss'
+ ELSE
!el ind=ind+1
itypj=itype(j)
if (itypj.eq.ntyp1) cycle
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot) &
+ .and.(zj.lt.bordliptop)) then
+!C the energy transfer exist
+ if (zj.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((zj-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+ +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+ +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
zj_safe=zj
subchap=0
+
do xshift=-1,1
do yshift=-1,1
do zshift=-1,1
!---------------------------------------------------------------
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
evdw=evdw+evdwij*sss*sss_ele_cut
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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,&
epsi,sigm,chi1,chi2,chip1,chip2,&
! Calculate angular part of the gradient.
call sc_grad_scale(sss)
endif
+ ENDIF !mask_dyn_ss
enddo ! j
enddo ! iint
enddo ! i
!---------------------------------------------------------------
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+(evdwij+e_augm)*(1.0d0-sss)
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
!---------------------------------------------------------------
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_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
evdwij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=evdwij*eps3rt
eps3der=evdwij*eps2rt
evdwij=evdwij*eps2rt*eps3rt
evdw=evdw+(evdwij+e_augm)*sss
if (lprn) then
- sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
- epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
+ sigm=dabs(aa_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,&
epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),&
#ifdef TIMING
time01=MPI_Wtime()
#endif
+! print *, "before set matrices"
call set_matrices
+! print *,"after set martices"
#ifdef TIMING
time_mat=time_mat+MPI_Wtime()-time01
#endif
! include 'COMMON.SCCOR'
!
!el local variables
- integer :: i,j,intertyp
+ integer :: i,j,intertyp,k
! Initialize Cartesian-coordinate gradient
!
! if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2)
! allocate(gloc_sc(3,nres,10)) !(3,0:maxres2,10)maxres2=2*maxres
!elwrite(iout,*) "icg",icg
- do i=1,nres
+ do i=-1,nres
do j=1,3
gvdwx(j,i)=0.0D0
gradx_scp(j,i)=0.0D0
gradx(j,i,icg)=0.0d0
gscloc(j,i)=0.0d0
gsclocx(j,i)=0.0d0
+ gliptran(j,i)=0.0d0
+ gshieldx(j,i)=0.0d0
+ gshieldc(j,i)=0.0d0
+ gshieldc_loc(j,i)=0.0d0
+ gshieldx_ec(j,i)=0.0d0
+ gshieldc_ec(j,i)=0.0d0
+ gshieldc_loc_ec(j,i)=0.0d0
+ gshieldx_t3(j,i)=0.0d0
+ gshieldc_t3(j,i)=0.0d0
+ gshieldc_loc_t3(j,i)=0.0d0
+ gshieldx_t4(j,i)=0.0d0
+ gshieldc_t4(j,i)=0.0d0
+ gshieldc_loc_t4(j,i)=0.0d0
+ gshieldx_ll(j,i)=0.0d0
+ gshieldc_ll(j,i)=0.0d0
+ gshieldc_loc_ll(j,i)=0.0d0
+
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo
enddo
enddo
+ do i=1,nres
+ do j=1,maxcontsshi
+ shield_list(j,i)=0
+ do k=1,3
+!C print *,i,j,k
+ grad_shield_side(k,j,i)=0.0d0
+ grad_shield_loc(k,j,i)=0.0d0
+ enddo
+ enddo
+ ishield_list(i)=0
+ enddo
+
!
! Initialize the gradient of local energy terms.
!
ljXs=sig-sig0ij
ljA=eps1*eps2rt**2*eps3rt**2
- ljB=ljA*bb(itypi,itypj)
- ljA=ljA*aa(itypi,itypj)
- ljxm=ljXs+(-2.0D0*aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
+ ljB=ljA*bb_aq(itypi,itypj)
+ ljA=ljA*aa_aq(itypi,itypj)
+ ljxm=ljXs+(-2.0D0*aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0)
ssXs=d0cm
deltat1=1.0d0-om1
! Stop and plot energy and derivative as a function of distance
if (checkstop) then
ssm=ssC-0.25D0*ssB*ssB/ssA
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
+ ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
if (ssm.lt.ljm .and. &
dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
nicheck=1000
havebond=.false.
ljd=rij-ljXs
fac=(1.0D0/ljd)**expon
- e1=fac*fac*aa(itypi,itypj)
- e2=fac*bb(itypi,itypj)
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
eij=eps1*eps2rt*eps3rt*(e1+e2)
eps2der=eij*eps3rt
eps3der=eij*eps2rt
eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
else
havebond=.false.
- ljm=-0.25D0*ljB*bb(itypi,itypj)/aa(itypi,itypj)
- d_ljm(1)=-0.5D0*bb(itypi,itypj)/aa(itypi,itypj)*ljB
+ ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
+ d_ljm(1)=-0.5D0*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)*ljB
d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt- &
alf12/eps3rt)
return
end subroutine dyn_set_nss
+! Lipid transfer energy function
+ subroutine Eliptransfer(eliptran)
+!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
+ real(kind=8) :: fracinbuf,eliptran,sslip,positi,ssgradlip
+ integer :: i
+ eliptran=0.0
+ 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))&
+ cycle
+
+ positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
+ if (positi.le.0.0) positi=positi+boxzsize
+!C print *,i
+!C first for peptide groups
+!c for each residue check if it is in lipid or lipid water border area
+ if ((positi.gt.bordlipbot) &
+ .and.(positi.lt.bordliptop)) then
+!C the energy transfer exist
+ if (positi.lt.buflipbot) then
+!C what fraction I am in
+ fracinbuf=1.0d0- &
+ ((positi-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+!C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+
+!C print *,"doing sccale for lower part"
+!C print *,i,sslip,fracinbuf,ssgradlip
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*pepliptran
+ gliptranc(3,i)=gliptranc(3,i)+ssgradlip*pepliptran/2.0d0
+ gliptranc(3,i-1)=gliptranc(3,i-1)+ssgradlip*pepliptran/2.0d0
+!C gliptranc(3,i-2)=gliptranc(3,i)+ssgradlip*pepliptran
+!C print *, "doing sscalefor top part"
+!C print *,i,sslip,fracinbuf,ssgradlip
+ else
+ eliptran=eliptran+pepliptran
+!C print *,"I am in true lipid"
+ endif
+!C else
+!C eliptran=elpitran+0.0 ! I am in water
+ endif
+ if (energy_dec) write(iout,*) i,"eliptran=",eliptran,positi,sslip
+ enddo
+! here starts the side chain transfer
+ do i=ilip_start,ilip_end
+ if (itype(i).eq.ntyp1) cycle
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+!C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+!c for each residue check if it is in lipid or lipid water border area
+!C respos=mod(c(3,i+nres),boxzsize)
+!C print *,positi,bordlipbot,buflipbot
+ if ((positi.gt.bordlipbot) &
+ .and.(positi.lt.bordliptop)) then
+!C the energy transfer exist
+ if (positi.lt.buflipbot) then
+ fracinbuf=1.0d0- &
+ ((positi-bordlipbot)/lipbufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=-sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i) &
+ +ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1) &
+ +ssgradlip*liptranene(itype(i))
+!C print *,"doing sccale for lower part"
+ elseif (positi.gt.bufliptop) then
+ fracinbuf=1.0d0- &
+ ((bordliptop-positi)/lipbufthick)
+ sslip=sscalelip(fracinbuf)
+ ssgradlip=sscagradlip(fracinbuf)/lipbufthick
+ eliptran=eliptran+sslip*liptranene(itype(i))
+ gliptranx(3,i)=gliptranx(3,i) &
+ +ssgradlip*liptranene(itype(i))
+ gliptranc(3,i-1)= gliptranc(3,i-1) &
+ +ssgradlip*liptranene(itype(i))
+!C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ eliptran=eliptran+liptranene(itype(i))
+!C print *,"I am in true lipid"
+ endif
+ endif ! if in lipid or buffor
+!C else
+!C eliptran=elpitran+0.0 ! I am in water
+ if (energy_dec) write(iout,*) i,"eliptran=",eliptran
+ enddo
+ return
+ end subroutine Eliptransfer
+!--------------------------------------------------------------------------------
+!C first for shielding is setting of function of side-chains
+
+ subroutine set_shield_fac2
+ real(kind=8) :: div77_81=0.974996043d0, &
+ div4_81=0.2222222222d0
+ real (kind=8) :: dist_pep_side,dist_side_calf,dist_pept_group, &
+ scale_fac_dist,fac_help_scale,VofOverlap,VolumeTotal,costhet,&
+ short,long,sinthet,costhet_fac,sh_frac_dist,rkprim,cosphi, &
+ sinphi,cosphi_fac,pep_side0pept_group,cosalfa,fac_alfa_sin
+!C the vector between center of side_chain and peptide group
+ real(kind=8),dimension(3) :: pep_side_long,side_calf, &
+ pept_group,costhet_grad,cosphi_grad_long, &
+ cosphi_grad_loc,pep_side_norm,side_calf_norm, &
+ sh_frac_dist_grad,pep_side
+ integer i,j,k
+!C write(2,*) "ivec",ivec_start,ivec_end
+ do i=1,nres
+ fac_shield(i)=0.0d0
+ do j=1,3
+ grad_shield(j,i)=0.0d0
+ enddo
+ 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
+ ishield_list(i)=0
+ if ((itype(i).eq.ntyp1).and.itype(i+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
+ 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=sqrt(dist_pep_side)
+ dist_pept_group=sqrt(dist_pept_group)
+ dist_side_calf=sqrt(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 print *,ishield_list(i),i
+!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
+ 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)
+
+ write(2,*) "TOTAL VOLUME",i,itype(i),fac_shield(i)
+ enddo
+ return
+ end subroutine set_shield_fac2
+
!-----------------------------------------------------------------------------
#ifdef WHAM
subroutine read_ssHist
allocate(grij_hb_cont(3,maxconts,nres))
!(3,maxconts,maxres)
allocate(facont_hb(maxconts,nres))
+
allocate(ees0p(maxconts,nres))
allocate(ees0m(maxconts,nres))
allocate(d_cont(maxconts,nres))
+ allocate(ees0plist(maxconts,nres))
+
!(maxconts,maxres)
allocate(num_cont_hb(nres))
!(maxres)
!(6,maxdim)
allocate(dxds(6,nres))
!(6,maxres)
- allocate(gradx(3,nres,0:2))
- allocate(gradc(3,nres,0:2))
+ allocate(gradx(3,-1:nres,0:2))
+ allocate(gradc(3,-1:nres,0:2))
!(3,maxres,2)
- allocate(gvdwx(3,nres))
- allocate(gvdwc(3,nres))
- allocate(gelc(3,nres))
- allocate(gelc_long(3,nres))
- allocate(gvdwpp(3,nres))
- allocate(gvdwc_scpp(3,nres))
- allocate(gradx_scp(3,nres))
- allocate(gvdwc_scp(3,nres))
- allocate(ghpbx(3,nres))
- allocate(ghpbc(3,nres))
- allocate(gradcorr(3,nres))
- allocate(gradcorr_long(3,nres))
- allocate(gradcorr5_long(3,nres))
- allocate(gradcorr6_long(3,nres))
- allocate(gcorr6_turn_long(3,nres))
- allocate(gradxorr(3,nres))
- allocate(gradcorr5(3,nres))
- allocate(gradcorr6(3,nres))
+ allocate(gvdwx(3,-1:nres))
+ allocate(gvdwc(3,-1:nres))
+ allocate(gelc(3,-1:nres))
+ allocate(gelc_long(3,-1:nres))
+ allocate(gvdwpp(3,-1:nres))
+ allocate(gvdwc_scpp(3,-1:nres))
+ allocate(gradx_scp(3,-1:nres))
+ allocate(gvdwc_scp(3,-1:nres))
+ allocate(ghpbx(3,-1:nres))
+ allocate(ghpbc(3,-1:nres))
+ allocate(gradcorr(3,-1:nres))
+ allocate(gradcorr_long(3,-1:nres))
+ allocate(gradcorr5_long(3,-1:nres))
+ allocate(gradcorr6_long(3,-1:nres))
+ allocate(gcorr6_turn_long(3,-1:nres))
+ allocate(gradxorr(3,-1:nres))
+ allocate(gradcorr5(3,-1:nres))
+ allocate(gradcorr6(3,-1:nres))
+ allocate(gliptran(3,-1:nres))
+ allocate(gliptranc(3,-1:nres))
+ allocate(gliptranx(3,-1:nres))
+ allocate(gshieldx(3,-1:nres))
+ allocate(gshieldc(3,-1:nres))
+ allocate(gshieldc_loc(3,-1:nres))
+ allocate(gshieldx_ec(3,-1:nres))
+ allocate(gshieldc_ec(3,-1:nres))
+ allocate(gshieldc_loc_ec(3,-1:nres))
+ allocate(gshieldx_t3(3,-1:nres))
+ allocate(gshieldc_t3(3,-1:nres))
+ allocate(gshieldc_loc_t3(3,-1:nres))
+ allocate(gshieldx_t4(3,-1:nres))
+ allocate(gshieldc_t4(3,-1:nres))
+ allocate(gshieldc_loc_t4(3,-1:nres))
+ allocate(gshieldx_ll(3,-1:nres))
+ allocate(gshieldc_ll(3,-1:nres))
+ allocate(gshieldc_loc_ll(3,-1:nres))
+ allocate(grad_shield(3,-1:nres))
!(3,maxres)
+ allocate(grad_shield_side(3,50,nres))
+ allocate(grad_shield_loc(3,50,nres))
+! grad for shielding surroing
allocate(gloc(0:maxvar,0:2))
allocate(gloc_x(0:maxvar,2))
!(maxvar,2)
- allocate(gel_loc(3,nres))
- allocate(gel_loc_long(3,nres))
- allocate(gcorr3_turn(3,nres))
- allocate(gcorr4_turn(3,nres))
- allocate(gcorr6_turn(3,nres))
- allocate(gradb(3,nres))
- allocate(gradbx(3,nres))
+ allocate(gel_loc(3,-1:nres))
+ allocate(gel_loc_long(3,-1:nres))
+ allocate(gcorr3_turn(3,-1:nres))
+ allocate(gcorr4_turn(3,-1:nres))
+ allocate(gcorr6_turn(3,-1:nres))
+ allocate(gradb(3,-1:nres))
+ allocate(gradbx(3,-1:nres))
!(3,maxres)
allocate(gel_loc_loc(maxvar))
allocate(gel_loc_turn3(maxvar))
allocate(g_corr5_loc(maxvar))
allocate(g_corr6_loc(maxvar))
!(maxvar)
- allocate(gsccorc(3,nres))
- allocate(gsccorx(3,nres))
+ allocate(gsccorc(3,-1:nres))
+ allocate(gsccorx(3,-1:nres))
!(3,maxres)
- allocate(gsccor_loc(nres))
+ allocate(gsccor_loc(-1:nres))
!(maxres)
- allocate(dtheta(3,2,nres))
+ allocate(dtheta(3,2,-1:nres))
!(3,2,maxres)
- allocate(gscloc(3,nres))
- allocate(gsclocx(3,nres))
+ allocate(gscloc(3,-1:nres))
+ allocate(gsclocx(3,-1:nres))
!(3,maxres)
- allocate(dphi(3,3,nres))
- allocate(dalpha(3,3,nres))
- allocate(domega(3,3,nres))
+ allocate(dphi(3,3,-1:nres))
+ allocate(dalpha(3,3,-1:nres))
+ allocate(domega(3,3,-1:nres))
!(3,3,maxres)
! common /deriv_scloc/
allocate(dXX_C1tab(3,nres))
!----------------------
! common.MD
! common /mdgrad/
- allocate(gcart(3,0:nres))
- allocate(gxcart(3,0:nres))
+ allocate(gcart(3,-1:nres))
+ allocate(gxcart(3,-1:nres))
!(3,0:MAXRES)
- allocate(gradcag(3,nres))
- allocate(gradxag(3,nres))
+ allocate(gradcag(3,-1:nres))
+ allocate(gradxag(3,-1:nres))
!(3,MAXRES)
! common /back_constr/
!el in energy:Econstr_back allocate((:),allocatable :: utheta,ugamma,uscdiff !(maxfrag_back)
allocate(idssb(nss),jdssb(nss))
!(maxdim)
endif
+ allocate(ishield_list(nres))
+ allocate(shield_list(50,nres))
allocate(dyn_ss_mask(nres))
+ allocate(fac_shield(nres))
!(maxres)
dyn_ss_mask(:)=.false.
!----------------------
projects / unres4.git / commitdiff