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+4.87567E-01 4.36438E+00 -1.00079E-01 0.00000E+00 -6.23208E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 SeMet_Wat
+3.94000E-02 5.02694E+00 1.42243E-02 0.00000E+00 -6.83672E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 DapBz_Wat
+3.38861E-01 4.80831E+00 -7.06324E-01 0.00000E+00 -1.79590E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Aib_Wat
+3.38861E-01 4.80831E+00 -7.06324E-01 0.00000E+00 -1.79590E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Abu_Wat
+3.50339E-01 4.85725E+00 -5.88844E-01 0.00000E+00 -1.28830E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 3.31407E-03 1.04186E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Glu_Wat
+3.50339E-01 4.85725E+00 -5.88844E-01 0.00000E+00 -1.28830E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 3.31407E-03 1.04186E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Glu_Wat
+2.66525E-01 3.95618E+00 -5.07160E-01 0.00000E+00 -7.07736E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 -4.51793E-01 8.14863E-02 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Asp_Wat
mnum=molnum(i)
iti=iabs(itype(i,mnum))
if (mnum.eq.5) iti=itype(i,mnum)
+! if (itype(i,mnum).eq.ntyp1_molec(mnum)) then
+! do j=1,3
+! incr(j)=d_t(j,i)
+! enddo
+! endif
if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
.or.mnum.ge.3) then
do j=1,3
mnum=molnum(i)
if (itype(i,mnum).ne.ntyp1_molec(mnum)&
.and.itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
- if (mnum.eq.5) Ip(mnum)=Isc(itype(i,mnum),mnum)
+ if (mnum.eq.5) Ip(mnum)=0.0
! write (iout,*) "i",i
! write (iout,*) "i",i," mag1",mag1," mag2",mag2
do j=1,3
do i=innt,inct-1
mnum=molnum(i)
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
- if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+ if (mnum.eq.5) mp(mnum)=0.0d0
+! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
!c write (iout,*) i,(d_t(j,i),j=1,3),(d_t(j,i+1),j=1,3)
do j=1,3
v(j)=0.5d0*(d_t(j,i)+d_t(j,i+1))
!c to the velocities of the first Calpha.
do i=innt,inct
mnum=molnum(i)
+ if (mnum.eq.5) then
+ iti=itype(i,mnum)
+ else
iti=iabs(itype(i,mnum))
+ endif
if (itype(i,1).eq.10.or.mnum.ge.3.or. itype(i,mnum).eq.ntyp1_molec(mnum)) then
!c write (iout,*) i,iti,(d_t(j,i),j=1,3)
do j=1,3
do j=1,3
incr(j)=d_t(j,i+1)-d_t(j,i)
enddo
- if (mnum.eq.5) Ip(mnum)=Isc(itype(i,mnum),mnum)
+ if (mnum.eq.5) Ip(mnum)=0.0d0
!c write (iout,*) i,(incr(j),j=1,3)
!c write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
KEr_p=KEr_p+Ip(mnum)*(incr(1)*incr(1)+incr(2)*incr(2)&
!c The rotational part of the side chain virtual bond
do i=innt,inct
mnum=molnum(i)
- iti=iabs(itype(i,mnum))
+! iti=iabs(itype(i,mnum))
+ if (mnum.eq.5) then
+ iti=itype(i,mnum)
+ else
+ iti=iabs(itype(i,mnum))
+ endif
+
! if (iti.ne.10.and.mnum.lt.3) then
if (itype(i,1).ne.10.and.mnum.lt.3.and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
do j=1,3
write (tytul,'("time",f8.2)') totT
if(mdpdb) then
+ write(iout,*) "before hairpin"
call hairpin(.true.,nharp,iharp)
+ write(iout,*) "before secondary"
call secondary2(.true.)
+ write(iout,*) "before pdbout"
call pdbout(potE,tytul,ipdb)
! call enerprint(potEcomp)
else
! call ginv_mult(fric_work, d_af_work)
! call ginv_mult(stochforcvec, d_as_work)
#ifdef FIVEDIAG
+ write(iout,*) "forces before fivediaginv"
+ do i=1,dimen*3
+ write(iout,*) "fricwork",i,fric_work(i)
+ enddo
call fivediaginv_mult(dimen,fric_work, d_af_work)
call fivediaginv_mult(dimen,stochforcvec, d_as_work)
if (large) then
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- real(kind=8),dimension(6*nres) :: stochforcvec,d_as_work1 !(MAXRES6) maxres6=6*maxres
+ real(kind=8),dimension(:),allocatable :: stochforcvec,d_as_work1 !(MAXRES6) maxres6=6*maxres
real(kind=8) :: cos60 = 0.5d0, sin60 = 0.86602540378443864676d0
integer :: i,j,ind,inres,mnum
+ if (.not.allocated(stochforcvec)) allocate(stochforcvec(6*nres))
+ if (.not.allocated(d_as_work1)) allocate(d_as_work1(6*nres))
! Revised 3/31/05 AL: correlation between random contributions to
! position and velocity increments included.
! The correlation coefficients are calculated at low-friction limit.
! include 'COMMON.TIME1'
real(kind=8) :: xv,sigv,lowb,highb ,Ek1
#ifdef FIVEDIAG
- integer ichain,n,innt,inct,ibeg,ierr
+ integer ichain,n,innt,inct,ibeg,ierr,innt_org
real(kind=8) ,allocatable, dimension(:):: work
integer,allocatable,dimension(:) :: iwork
! double precision Ghalf(mmaxres2_chain),Geigen(maxres2_chain),&
EK=0.0d0
Ek3=0.0d0
#ifdef DEBUG
- write(iout,*), nchain
+ write(iout,*), "nchain",nchain
#endif
do ichain=1,nchain
ind=0
! ghalf=0.0d0
n=dimen_chain(ichain)
innt=iposd_chain(ichain)
- if (molnum(innt).eq.5) go to 137
+! innt_org=
+ innt_org=chain_border(1,ichain)
+ if ((molnum(innt_org).eq.5).or.(molnum(innt_org).eq.4)) go to 137
if(.not.allocated(ghalf)) print *,"COCO"
if(.not.allocated(Ghalf)) allocate(Ghalf(1300*(1300+1)/2))
ghalf=0.0d0
enddo
#endif
137 continue
- write(iout,*) "HERE,",n
+ write(iout,*) "HERE,",n,innt
+ innt_org=chain_border(1,ichain)
xv=0.0d0
ii=0
do i=1,n
do k=1,3
ii=ii+1
- if (molnum(innt).eq.5) geigen(i)=1.0/msc(itype(innt+i-1,5),5)
-
+ mnum=molnum(innt_org)
+ if (molnum(innt_org).ge.4) geigen(i)=3.0/msc(itype(innt_org+i-1,mnum),mnum)
+! if (molnum(innt).eq.5) write(iout,*) "typ",i,innt-1+i,itype(innt+i-1,5)
sigv=dsqrt((Rb*t_bath)/geigen(i))
lowb=-5*sigv
highb=5*sigv
d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
EK=EK+0.5d0*geigen(i)*d_t_work_new(ii)**2
-! write (iout,*) "i",i," ii",ii," geigen",geigen(i), &
-! " d_t_work_new",d_t_work_new(ii)
+ write (iout,*) "i",i," ii",ii," geigen",geigen(i), &
+ " d_t_work_new",d_t_work_new(ii),innt_org+i-1
enddo
enddo
- if (molnum(innt).eq.5) then
-
+ if (molnum(innt_org).ge.4) then
+ mnum=molnum(innt_org)
do k=1,3
do i=1,n
ind=(i-1)*3+k
d_t_work(ind)=0.0d0
- masinv=1.0/msc(itype(innt+i-1,5),5)
+ masinv=1.0d0/msc(itype(innt_org+i-1,mnum),mnum)
d_t_work(ind)=d_t_work(ind)&
+masinv*d_t_work_new((i-1)*3+k)
enddo
d_t(:,0)=d_t(:,1)
d_t(:,1)=0.0d0
endif
+ if (large) then
+ write (iout,*)
+ write (iout,*) "Random vel after 1st transf the Calpha,SC space"
+ write (iout,'(3hORG,1h(,i5,1h),3f10.5)') 0,(d_t(j,0),j=1,3)
+ do i=1,nres
+ mnum=molnum(i)
+ write (iout,'(a3,1h(,i5,1h),3f10.5,3x,3f10.5)')&
+ restyp(itype(i,mnum),mnum),i,(d_t(j,i),j=1,3),(d_t(j,i+nres),j=1,3)
+ enddo
+ endif
+
!c d_a(:,0)=d_a(:,1)
!c d_a(:,1)=0.0d0
!c write (iout,*) "Shifting accelerations"
do ichain=2,nchain
+ write(iout,*) "nchain",ichain,chain_border1(1,ichain),molnum(chain_border1(1,ichain))
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
!c write (iout,*) "ichain",chain_border1(1,ichain)-1,
!c & chain_border1(1,ichain)
d_t(:,chain_border1(1,ichain)-1)=d_t(:,chain_border1(1,ichain))
enddo
!c write (iout,*) "Adding accelerations"
do ichain=2,nchain
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
!c write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
!c & chain_border(2,ichain-1)
d_t(:,chain_border1(1,ichain)-1)=&
do ichain=2,nchain
write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,&
chain_border(2,ichain-1)
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
+
d_t(:,chain_border1(1,ichain)-1)=&
d_t(:,chain_border1(1,ichain)-1)+d_t(:,chain_border(2,ichain-1))
d_t(:,chain_border(2,ichain-1))=0.0d0
enddo
+ if (large) then
+ write (iout,*)
+ write (iout,*) "Random vel after 2nd transf the Calpha,SC space"
+ write (iout,'(3hORG,1h(,i5,1h),3f10.5)') 0,(d_t(j,0),j=1,3)
+ do i=1,nres
+ mnum=molnum(i)
+ write (iout,'(a3,1h(,i5,1h),3f10.5,3x,3f10.5)')&
+ restyp(itype(i,mnum),mnum),i,(d_t(j,i),j=1,3),(d_t(j,i+nres),j=1,3)
+ enddo
+ endif
+
#else
ibeg=0
!c do j=1,3
M_PEP=0.0d0
do i=nnt,nct-1
mnum=molnum(i)
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
write(iout,*) "WTF",itype(i,mnum),i,mnum,mp(mnum)
! if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
M_PEP=M_PEP+mp(mnum)
M_SC=0.0d0
do i=nnt,nct
mnum=molnum(i)
- if (mnum.ge.5) cycle
+! if (mnum.ge.5) cycle
iti=iabs(itype(i,mnum))
M_SC=M_SC+msc(iabs(iti),mnum)
inres=i+nres
+ if (mnum.ge.4) inres=i
do j=1,3
cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)
enddo
! write(iout,*) "Center of mass:",cm
do i=nnt,nct-1
mnum=molnum(i)
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
do j=1,3
pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
enddo
do i=nnt,nct
mnum=molnum(i)
iti=iabs(itype(i,mnum))
- if (mnum.ge.5) cycle
+! if (mnum.ge.5) cycle
inres=i+nres
+ if (mnum.ge.4) inres=i
do j=1,3
pr(j)=c(j,inres)-cm(j)
enddo
summas=0.0d0
do i=nnt,nct
mnum=molnum(i)
- if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+! if (mnum.ge.4) mp(mnum)=msc(itype(i,mnum),mnum)
if (i.lt.nct) then
summas=summas+mp(mnum)
do j=1,3
! print *,i,j,vv(j),d_t(j,i)
enddo
endif
- if (mnum.ne.4) then
+! if (mnum.ne.4) then
amas=msc(iabs(itype(i,mnum)),mnum)
- else
- amas=0.0d0
- endif
+! else
+! amas=0.0d0
+! endif
summas=summas+amas
if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
.and.(mnum.lt.4)) then
!c innt=chain_border(1,1)
!c inct=chain_border(2,1)
do i=innt,inct
+ mnum=molnum(i)
vvec(ind+1)=v_work(j,i)
ind=ind+1
! if (iabs(itype(i)).ne.10) then
! include 'COMMON.IOUNITS'
integer :: IERROR
integer :: i,j,ind,ind1,m,ichain,innt,inct
- logical :: lprn = .false.
+ logical :: lprn = .true.
real(kind=8) :: dtdi !el ,gamvec(2*nres)
!el real(kind=8),dimension(2*nres,2*nres) :: ginvfric,fcopy
! real(kind=8),allocatable,dimension(:,:) :: fcopy
enddo
!c DU1fric part
do ichain=1,nchain
- mnum=molnum(i)
-
ind=iposd_chain(ichain)
innt=chain_border(1,ichain)
inct=chain_border(2,ichain)
do i=innt,inct
+ mnum=molnum(i)
if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
ind=ind+2
else
enddo
!c DU2fric part
do ichain=1,nchain
- mnum=molnum(i)
ind=iposd_chain(ichain)
innt=chain_border(1,ichain)
inct=chain_border(2,ichain)
do i=innt,inct-1
+ mnum=molnum(i)
if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
DU2fric(ind)=gamvec(i-nnt+1)/4
DU2fric(ind+1)=0.0d0
! the line below might be wrong
#ifdef FIVEDIAG
real(kind=8) :: rs(2*nres),xsolv(2*nres)
-#ifdef CHECK5DSOL
+!#ifdef CHECK5DSOL
real(kind=8) :: rscheck(2*nres),rsold(2*nres)
-#endif
+!#endif
#endif
logical :: lprn = .false.
!el common /cipiszcze/ itime
endif
#ifdef CHECK5DSOL
! Check the solution
- call fivediagmult(n,DMorig(innt),DU1orig(innt),DU2orig(innt),
- & xsolv,rscheck)
+ call fivediagmult(n,DMorig(innt),DU1orig(innt),DU2orig(innt),&
+ xsolv,rscheck)
do i=1,n
- write(iout,*) "i",i,"rsold",rsold(i),"rscheck",rscheck(i),
- & "ratio",rscheck(i)/rsold(i)
+ write(iout,*) "i",i,"rsold",rsold(i),"rscheck",rscheck(i),&
+ "ratio",rscheck(i)/rsold(i)
enddo
! end check
#endif
#define CHUJ
#ifdef CHUJ
do ichain=2,nchain
+!TEST 27.06.2023 godz 16.00
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
!c write (iout,*) "ichain",chain_border1(1,ichain)-1,
!c & chain_border1(1,ichain)
d_a(:,chain_border1(1,ichain)-1)=d_a(:,chain_border1(1,ichain))
enddo
!c write (iout,*) "Adding accelerations"
do ichain=2,nchain
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
!c write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
!c & chain_border(2,ichain-1)
d_a(:,chain_border1(1,ichain)-1)=&
mnum=molnum(innt)
inct=chain_border(2,ichain)
if (mnum.eq.5) mp(mnum)=0.0
+ if (mnum.eq.5) ip(mnum)=0.0
! if (mnum.eq.5) mp(mnum)=msc(itype(innt,mnum),mnum)
DM(ind)=mp(mnum)/4+ip(mnum)/4
if (iabs(itype(innt,1)).eq.10.or.molnum(innt).gt.2) then
! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
! if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
if (mnum.eq.5) mp(mnum)=0.0
+ if (mnum.eq.5) ip(mnum)=0.0
! if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
DM(ind)=2*ip(mnum)/4+mp(mnum)/2
if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2) then
enddo
DMorig=DM
DU1orig=DU1
- DU2orig=DU2
+ DU2orig=DU2
+ gmatout=.true.
if (gmatout) then
write (iout,*)"The upper part of the five-diagonal inertia matrix"
endif
subroutine fivediaginv_mult(ndim,forces,d_a_vec)
use energy_data, only:nchain,chain_border,nct,nnt,molnum,&
chain_border1,itype
+ use geometry_data, only: nside
integer ndim
- double precision forces(3*ndim),accel(3,0:maxres2),rs(ndim), &
- xsolv(ndim),d_a_vec(6*nres)
+
+ real(kind=8),dimension(:),allocatable ::forces,d_a_vec
+ real(kind=8),dimension(:),allocatable :: xsolv,rs
+ real(kind=8),dimension(:,:),allocatable :: accel
integer i,j,ind,ichain,n,iposc,innt,inct,inct_prev,mnum
accel=0.0d0
+!#define DEBUG
+ if (.not.allocated(forces)) allocate(forces(6*nres))
+ if (.not.allocated(d_a_vec)) allocate(d_a_vec(6*nres))
+ if (.not.allocated(xsolv)) allocate(xsolv(3*ndim))
+ if (.not.allocated(rs)) allocate(rs(3*ndim))
+ if (.not.allocated(accel)) allocate(accel(3,0:2*nres))
+
+#ifdef DEBUG
+ do i=1,6*nres
+ write(iout,*) "received forces",i,forces(i)
+ enddo
+#endif
do j=1,3
!Compute accelerations in Calpha and SC
do ichain=1,nchain
innt=chain_border(1,ichain)
inct=chain_border(2,ichain)
do i=iposc,iposc+n-1
+! write(iout,*) "index",3*(i-1)+j,forces(3*(i-1)+j)
rs(i-iposc+1)=forces(3*(i-1)+j)
enddo
#ifdef DEBUG
- write (iout,*) "j",j," chain",ichain
+ write (iout,*) "j",j," chain",ichain,"n",n
+ write (iout,*) "innt",innt,inct,iposc
write (iout,*) "rs"
- write (iout,'(f10.5)') (rs(i),i=1,n)
+ do i=1,n
+ write (iout,'(i5,f10.5)') i,rs(i)
+ enddo
#endif
call FDISYS (n,DM(iposc),DU1(iposc),DU2(iposc),rs,xsolv)
#ifdef DEBUG
#ifdef DEBUG
write (iout,*) "accel in CA-SC basis"
do i=1,nres
- write (iout,'(i5,3f10.5,5x,3f10.5)') i,(accel(j,i),j=1,3),
- & (accel(j,i+nres),j=1,3)
+ write (iout,'(i5,3f10.5,5x,3f10.5)') i,(accel(j,i),j=1,3),&
+ (accel(j,i+nres),j=1,3)
enddo
write (iout,*) "nnt",nnt
#endif
accel(:,1)=0.0d0
endif
do ichain=2,nchain
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
accel(:,chain_border1(1,ichain)-1)= &
accel(:,chain_border1(1,ichain))
accel(:,chain_border1(1,ichain))=0.0d0
enddo
do ichain=2,nchain
+ if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
accel(:,chain_border1(1,ichain)-1)= &
accel(:,chain_border1(1,ichain)-1) &
+accel(:,chain_border(2,ichain-1))
#endif
return
end subroutine
-
+#undef DEBUG
#else
!-----------------------------------------------------------------------------
! include 'COMMON.FFIELD'
! include 'COMMON.NAMES'
integer :: ncont
- integer,dimension(2,100*nres) :: icont !(2,maxcont) (maxcont=12*maxres)
+ integer,dimension(:,:),allocatable :: icont !(2,maxcont) (maxcont=12*maxres)
integer :: nharp
integer,dimension(4,nres) :: iharp !(4,nres/3)(4,maxres/3)
logical :: lprint,not_done
real(kind=8) :: rcomp=6.0d0
!el local variables
integer :: i,j,kkk,k,i1,i2,it1,it2,j1,ii1,jj1
-! allocate(icont(2,100*nres))
-
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
ncont=0
kkk=0
! print *,'nnt=',nnt,' nct=',nct
real(kind=8) :: ael6_i,ael3_i
real(kind=8),dimension(2,2) :: app_,bpp_,rpp_
integer :: ncont
- integer,dimension(2,100*nres) :: icont !(2,100*nres)(2,maxcont) (maxcont=12*maxres)
- real(kind=8),dimension(100*nres) :: econt !(maxcont)
+ integer,dimension(:,:),allocatable :: icont !(2,100*nres)(2,maxcont) (maxcont=12*maxres)
+ real(kind=8),dimension(:),allocatable :: econt !(maxcont)
!el local variables
integer :: i,j,k,iteli,itelj,i1,i2,it1,it2,ic1,ic2
real(kind=8) :: elcutoff,elecutoff_14,rri,ees,evdw
data elpp_3 / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
!el allocate(econt(100*nres)) !(maxcont)
-
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
+ if (.not.allocated(econt)) then
+ allocate(econt(100*nres_molec(1)+1))
+ endif
elcutoff = -0.3d0
elecutoff_14 = -0.5d0
if (lprint) write (iout,'(a)') &
! include 'COMMON.CONTROL'
integer :: ncont,i,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,nhelix,&
iii1,jjj1
- integer,dimension(2,100*nres) :: icont !(2,maxcont) (maxcont=12*maxres)
+ integer,dimension(:,:),allocatable :: icont !(2,maxcont) (maxcont=12*maxres)
integer,dimension(nres,0:4) :: isec !(maxres,4)
integer,dimension(nres) :: nsec !(maxres)
logical :: lprint,not_done !,freeres
!el external freeres
!el allocate(icont(2,100*nres),isec(nres,4),nsec(nres))
-
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres+1))
+ endif
if(.not.dccart) call chainbuild_cart
if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
!d call write_pdb(99,'sec structure',0d0)
! include 'COMMON.IOUNITS'
! include 'COMMON.DISTFIT'
- integer :: ncont,icont(2,nres*nres/2),isec(nres,3)
+ integer :: ncont,isec(nres,3)
logical :: lprint,not_done
- real(kind=4) :: dcont(nres*nres/2),d
+ real(kind=4) :: d
real(kind=4) :: rcomp = 7.0
real(kind=4) :: rbeta = 5.2
real(kind=4) :: ralfa = 5.2
real(kind=8),dimension(3) :: xpi,xpj
integer :: i,k,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,iii1,jjj1,&
nhelix
+ integer, dimension(:,:),allocatable :: icont
+ real(kind=4),dimension(:),allocatable :: dcont
+ if (.not.allocated(icont)) then
+ allocate(icont(2,100*nres_molec(1)+1))
+ endif
+ if (.not.allocated(dcont)) then
+ allocate(dcont(100*nres_molec(1)+1))
+ endif
call chainbuild_cart
!d call write_pdb(99,'sec structure',0d0)
ncont=0
(xpi(2)-xpj(2))*(xpi(2)-xpj(2)) + &
(xpi(3)-xpj(3))*(xpi(3)-xpj(3))
if ( d.lt.rcomp*rcomp) then
+ if (ncont.gt.(100*nres_molec(1)+1)) ncont=100*nres_molec(1)+1
ncont=ncont+1
icont(1,ncont)=i
icont(2,ncont)=j
! print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
! write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
- gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k) &
+ gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k)*sss_ele_cut &
+(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
- +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+ +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut
! gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) &
! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) &
! Calculate the components of the gradient in DC and X
!
do l=1,3
- gradpepcat(l,i)=gradpepcat(l,i)-gg(l)
- gradpepcat(l,j)=gradpepcat(l,j)+gg(l)
+ gradpepcat(l,i)=gradpepcat(l,i)-gg(l)*sss_ele_cut
+ gradpepcat(l,j)=gradpepcat(l,j)+gg(l)*sss_ele_cut
enddo
end subroutine sc_grad_cat
! eom2=0.0d0
! eom12=evdwij*eps1_om12
! end diagnostics
+! write (iout,*) "gg",(gg(k),k=1,3)
do k=1,3
dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
- gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k)) &
+ gradpepcat(k,i)= gradpepcat(k,i) +sss_ele_cut*(0.5*(- gg(k)) &
+ (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
*dsci_inv*2.0 &
- - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
- gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k)) &
+ - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0)
+ gradpepcat(k,i+1)= gradpepcat(k,i+1) +sss_ele_cut*(0.5*(- gg(k)) &
- (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
*dsci_inv*2.0 &
- + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
- gradpepcat(k,j)=gradpepcat(k,j)+gg(k)
+ + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0)
+ gradpepcat(k,j)=gradpepcat(k,j)+gg(k)*sss_ele_cut
enddo
end subroutine sc_grad_cat_pep
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
dist_temp, dist_init,ssgradlipi,ssgradlipj, &
sslipi,sslipj,faclip,alpha_sco
- integer :: ii
+ integer :: ii,ki
real(kind=8) :: fracinbuf
real (kind=8) :: escpho
real (kind=8),dimension(4):: ener
enddo
! go to 17
! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization
- do i=ibond_start,ibond_end
+! do i=ibond_start,ibond_end
+ do ki=g_listcatscnorm_start,g_listcatscnorm_end
+ i=newcontlistcatscnormi(ki)
+ j=newcontlistcatscnormj(ki)
! print *,"I am in EVDW",i
itypi=iabs(itype(i,1))
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=vbld_inv(i+nres)
- do j=itmp+1,itmp+nres_molec(5)
+! do j=itmp+1,itmp+nres_molec(5)
! Calculate SC interaction energy.
itypj=iabs(itype(j,5))
zj=boxshift(zj-zi,boxzsize)
! write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
+ dxj=0.0
+ dyj=0.0
+ dzj=0.0
! dxj = dc_norm( 1, nres+j )
! dyj = dc_norm( 2, nres+j )
! dzj = dc_norm( 3, nres+j )
! rij holds 1/(distance of Calpha atoms)
rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
rij = dsqrt(rrij)
+ sss_ele_cut=sscale_ele(1.0d0/(rij))
+ sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+! print *,sss_ele_cut,sss_ele_grad,&
+! 1.0d0/(rij),r_cut_ele,rlamb_ele
+ if (sss_ele_cut.le.0.0) cycle
CALL sc_angular
! this should be in elgrad_init but om's are calculated by sc_angular
! which in turn is used by older potentials
! END IF
!#else
evdw = evdw &
- + evdwij
+ + evdwij*sss_ele_cut
!#endif
c1 = c1 * eps1 * eps2rt**2 * eps3rt**2
fac = -expon * (c1 + evdwij) * rij_shift
sigder = fac * sigder
! Calculate distance derivative
- gg(1) = fac
- gg(2) = fac
- gg(3) = fac
+ gg(1) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(2) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(3) = fac*sss_ele_cut+evdwij*sss_ele_grad
! print *,"GG(1),distance grad",gg(1)
fac = chis1 * sqom1 + chis2 * sqom2 &
- 2.0d0 * chis12 * om1 * om2 * om12
dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
dbot = 12.0d0 * b4cav * bat * Lambf
- dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+&
+ Fcav*sss_ele_grad
+ Fcav=Fcav*sss_ele_cut
dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
dbot = 12.0d0 * b4cav * bat * Chif
eagle = Lambf * pom
isel = iabs(Qi) + 1 ! ion is always charged so iabs(Qj)
! print *,i,itype(i,1),isel
IF (isel.eq.0) THEN
-!c! No charges - do nothing
eheadtail = 0.0d0
-
ELSE IF (isel.eq.1) THEN
-!c! Nonpolar-charge interactions
if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
Qi=Qi*2
Qij=Qij*2
endif
-
CALL enq_cat(epol)
eheadtail = epol
-! eheadtail = 0.0d0
-
ELSE IF (isel.eq.3) THEN
-!c! Dipole-charge interactions
if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
Qi=Qi*2
Qij=Qij*2
endif
-! write(iout,*) "KURWA0",d1
-
CALL edq_cat(ecl, elj, epol)
eheadtail = ECL + elj + epol
-! eheadtail = 0.0d0
-
ELSE IF ((isel.eq.2)) THEN
-
-!c! Same charge-charge interaction ( +/+ or -/- )
if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
Qi=Qi*2
Qij=Qij*2
endif
-
CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj)
eheadtail = ECL + Egb + Epol + Fisocav + Elj
-! eheadtail = 0.0d0
-
-! ELSE IF ((isel.eq.2.and. &
-! iabs(Qi).eq.1).and. &
-! nstate(itypi,itypj).ne.1) THEN
-!c! Different charge-charge interaction ( +/- or -/+ )
-! if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-! Qi=Qi*2
-! Qij=Qij*2
-! endif
-! if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-! Qj=Qj*2
-! Qij=Qij*2
-! endif
-!
-! CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
END IF ! this endif ends the "catch the gly-gly" at the beggining of Fcav
- else
- write(iout,*) "not yet implemented",j,itype(j,5)
+ else ! here is water and other molecules
+ isel = iabs(Qi)+2
+! isel=2
+! if (isel.eq.4) isel=2
+ if (isel.eq.2) then
+ eheadtail = 0.0d0
+ else if (isel.eq.3) then
+ if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+ Qi=Qi*2
+ Qij=Qij*2
+ endif
+ call eqd_cat(ecl,elj,epol)
+ eheadtail = ECL + elj + epol
+ else if (isel.eq.4) then
+ call edd_cat(ecl)
+ eheadtail = ECL
+ endif
+! write(iout,*) "not yet implemented",j,itype(j,5)
endif
!! endif ! turn off electrostatic
evdw = evdw + Fcav + eheadtail
!c!-------------------------------------------------------------------
!c! NAPISY KONCOWE
END DO ! j
- END DO ! i
+! END DO ! i
!c write (iout,*) "Number of loop steps in EGB:",ind
!c energy_dec=.false.
! print *,"EVDW KURW",evdw,nres
!!! return
17 continue
! go to 23
- do i=ibond_start,ibond_end
+! do i=ibond_start,ibond_end
+
+ do ki=g_listcatpnorm_start,g_listcatpnorm_end
+ i=newcontlistcatpnormi(ki)
+ j=newcontlistcatpnormj(ki)
! print *,"I am in EVDW",i
itypi=10 ! the peptide group parameters are for glicine
dyi=dc_norm(2,i)
dzi=dc_norm(3,i)
dsci_inv=vbld_inv(i+1)/2.0
- do j=itmp+1,itmp+nres_molec(5)
+! do j=itmp+1,itmp+nres_molec(5)
! Calculate SC interaction energy.
itypj=iabs(itype(j,5))
dCAVdOM1 = 0.0d0
dCAVdOM2 = 0.0d0
dCAVdOM12 = 0.0d0
- dscj_inv = vbld_inv(j+nres)
+ dscj_inv = 0.0d0 ! vbld_inv(j+nres)
! print *,i,j,dscj_inv,dsci_inv
! rij holds 1/(distance of Calpha atoms)
rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
rij = dsqrt(rrij)
+ sss_ele_cut=sscale_ele(1.0d0/(rij))
+ sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+! print *,sss_ele_cut,sss_ele_grad,&
+! 1.0d0/(rij),r_cut_ele,rlamb_ele
+ if (sss_ele_cut.le.0.0) cycle
CALL sc_angular
! this should be in elgrad_init but om's are calculated by sc_angular
! which in turn is used by older potentials
! om = omega, sqom = om^2
+ om2=0.0d0
+ om12=0.0d0
sqom1 = om1 * om1
sqom2 = om2 * om2
sqom12 = om12 * om12
! END IF
!#else
evdw = evdw &
- + evdwij
+ + evdwij*sss_ele_cut
!#endif
c1 = c1 * eps1 * eps2rt**2 * eps3rt**2
fac = -expon * (c1 + evdwij) * rij_shift
sigder = fac * sigder
! Calculate distance derivative
- gg(1) = fac
- gg(2) = fac
- gg(3) = fac
+ gg(1) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(2) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(3) = fac*sss_ele_cut+evdwij*sss_ele_grad
fac = chis1 * sqom1 + chis2 * sqom2 &
- 2.0d0 * chis12 * om1 * om2 * om12
dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
dbot = 12.0d0 * b4cav * bat * Lambf
- dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+&
+ Fcav*sss_ele_grad
+ Fcav=Fcav*sss_ele_cut
dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
dbot = 12.0d0 * b4cav * bat * Chif
eagle = Lambf * pom
dFdOM1 = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
+
dFdOM2 = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
* (chis2 * om2 * om12 - om1) / (eagle * pom)
dFdL = ((dtop * bot - top * dbot) / botsq)
dCAVdOM1 = dFdL * ( dFdOM1 )
- dCAVdOM2 = dFdL * ( dFdOM2 )
- dCAVdOM12 = dFdL * ( dFdOM12 )
+! dCAVdOM2 = dFdL * ( dFdOM2 )
+! dCAVdOM12 = dFdL * ( dFdOM12 )
+ dCAVdOM2=0.0d0
+ dCAVdOM12=0.0d0
DO k= 1, 3
ertail(k) = Rtail_distance(k)/Rtail
! eheadtail = 0.0d0
else
!HERE WATER and other types of molecules solvents will be added
- write(iout,*) "not yet implemented"
+! write(iout,*) "not yet implemented"
+ CALL edd_cat_pep(ecl)
+ eheadtail=ecl
! CALL edd_cat_pep
+! eheadtail=0.0d0
endif
evdw = evdw + Fcav + eheadtail
! if (evdw.gt.1.0d6) then
!c!-------------------------------------------------------------------
!c! NAPISY KONCOWE
END DO ! j
- END DO ! i
+! END DO ! i
!c write (iout,*) "Number of loop steps in EGB:",ind
!c energy_dec=.false.
! print *,"EVDW KURW",evdw,nres
! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization
do i=ibond_start,ibond_end
! cycle
+
if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms
xi=0.5d0*(c(1,i)+c(1,i+1))
yi=0.5d0*(c(2,i)+c(2,i+1))
real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
dist_temp, dist_init,ssgradlipi,ssgradlipj, &
sslipi,sslipj,faclip,alpha_sco
- integer :: ii
+ integer :: ii,icont
real(kind=8) :: fracinbuf
real (kind=8) :: escpho
real (kind=8),dimension(4):: ener
sss_ele_cut=1.0d0
countss=0
! print *,"EVDW KURW",evdw,nres
- do i=iatsc_s,iatsc_e
+! do i=iatsc_s,iatsc_e
! print *,"I am in EVDW",i
+ do icont=g_listscsc_start,g_listscsc_end
+ i=newcontlisti(icont)
+ j=newcontlistj(icont)
+
itypi=iabs(itype(i,1))
! if (i.ne.47) cycle
if (itypi.eq.ntyp1) cycle
!
! Calculate SC interaction energy.
!
- do iint=1,nint_gr(i)
- do j=istart(i,iint),iend(i,iint)
+! do iint=1,nint_gr(i)
+! do j=istart(i,iint),iend(i,iint)
! print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
call dyn_ssbond_ene(i,j,evdwij,countss)
! rij holds 1/(distance of Calpha atoms)
rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
rij = dsqrt(rrij)
+ sss_ele_cut=sscale_ele(1.0d0/(rij))
+ sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+! print *,sss_ele_cut,sss_ele_grad,&
+! 1.0d0/(rij),r_cut_ele,rlamb_ele
+ if (sss_ele_cut.le.0.0) cycle
+
!----------------------------
CALL sc_angular
! this should be in elgrad_init but om's are calculated by sc_angular
! END IF
!#else
evdw = evdw &
- + evdwij
+ + evdwij*sss_ele_cut
!#endif
c1 = c1 * eps1 * eps2rt**2 * eps3rt**2
sigder = fac * sigder
! fac = rij * fac
! Calculate distance derivative
- gg(1) = fac
- gg(2) = fac
- gg(3) = fac
+ gg(1) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(2) = fac*sss_ele_cut+evdwij*sss_ele_grad
+ gg(3) = fac*sss_ele_cut+evdwij*sss_ele_grad
! if (b2.gt.0.0) then
fac = chis1 * sqom1 + chis2 * sqom2 &
- 2.0d0 * chis12 * om1 * om2 * om12
dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
dbot = 12.0d0 * b4cav * bat * Lambf
- dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut&
+ +Fcav*sss_ele_grad
+ Fcav=Fcav*sss
dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
dbot = 12.0d0 * b4cav * bat * Chif
eagle = Lambf * pom
END IF
!c!-------------------------------------------------------------------
!c! NAPISY KONCOWE
- END DO ! j
- END DO ! iint
+ ! END DO ! j
+ !END DO ! iint
END DO ! i
!c write (iout,*) "Number of loop steps in EGB:",ind
!c energy_dec=.false.
!c! Coulomb electrostatic interaction
Ecl = (332.0d0 * Qij) / Rhead
!c! derivative of Ecl is Gcl...
- dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+ dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad
dGCLdOM1 = 0.0d0
dGCLdOM2 = 0.0d0
dGCLdOM12 = 0.0d0
+ ECL=ECL*sss_ele_grad
ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
debkap=debaykap(itypi,itypj)
-(332.0d0 * Qij *&
(dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
- dGGBdR = dGGBdFGB * dFGBdR
+ dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+ Egb=Egb*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Fisocav - isotropic cavity creation term
!c! or "how much energy it costs to put charged head in water"
* ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
* ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
- dPOLdR1 = dPOLdFGB1 * dFGBdR1
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut
!c! dPOLdR1 = 0.0d0
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+ (ELJ+epol)*sss_ele_grad
+ epol=epol*sss_ele_cut
+ Elj=Elj*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c! These things do the dRdX derivatives, that is
!c! Coulomb electrostatic interaction
Ecl = (332.0d0 * Qij) / Rhead
!c! derivative of Ecl is Gcl...
- dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+ dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad
+ ECL=ECL*sss_ele_cut
dGCLdOM1 = 0.0d0
dGCLdOM2 = 0.0d0
dGCLdOM12 = 0.0d0
-(332.0d0 * Qij *&
(dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
- dGGBdR = dGGBdFGB * dFGBdR
+ dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+ Egb=Egb*sss_ele_grad
!c!-------------------------------------------------------------------
!c! Fisocav - isotropic cavity creation term
!c! or "how much energy it costs to put charged head in water"
!c! Derivative of Fisocav is GCV...
dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
dbot = 12.0d0 * al4 * pom ** 11.0d0
- dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+ dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut&
+ +FisoCav*sss_ele_grad
+ FisoCav=FisoCav*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Epol
!c! Polarization energy - charged heads polarize hydrophobic "neck"
* ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
* ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
- dPOLdR1 = dPOLdFGB1 * dFGBdR1
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1!*sss_ele_cut+epol*sss_ele_grad
!c! dPOLdR1 = 0.0d0
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2!*sss_ele_cut+epol*sss_ele_grad
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+! epol=epol*sss_ele_cut
!c! dPOLdOM2 = 0.0d0
!c!-------------------------------------------------------------------
!c! Elj
Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut&
+ +(Elj+epol)*sss_ele_grad
+ Elj=Elj*sss_ele_cut
+ epol=epol*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c! These things do the dRdX derivatives, that is
dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
!c! this acts on hydrophobic center of interaction
- gvdwx(k,i)= gvdwx(k,i) - gg(k) &
+ gvdwx(k,i)= gvdwx(k,i) - gg(k)*sss_ele_cut &
+ (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
- + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
- gvdwx(k,j)= gvdwx(k,j) + gg(k) &
+ + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut
+ gvdwx(k,j)= gvdwx(k,j) + gg(k)*sss_ele_cut &
+ (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))&
- + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+ + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut
!c! this acts on Calpha
- gvdwc(k,i)=gvdwc(k,i)-gg(k)
- gvdwc(k,j)=gvdwc(k,j)+gg(k)
+ gvdwc(k,i)=gvdwc(k,i)-gg(k)*sss_ele_cut
+ gvdwc(k,j)=gvdwc(k,j)+gg(k)*sss_ele_cut
END DO
!c! sc_grad is done, now we will compute
eheadtail = 0.0d0
!c! Ecl = 0.0d0
!c! write (*,*) "Ecl = ", Ecl
!c! derivative of Ecl is Gcl...
- dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
+ dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)*sss_ele_cut+ECL*sss_ele_grad
+ ECL=ecl*sss_ele_cut
!c! dGCLdR = 0.0d0
dGCLdOM1 = 0.0d0
dGCLdOM2 = 0.0d0
dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
/ ( 2.0d0 * Fgb )
- dGGBdR = dGGBdFGB * dFGBdR
+ dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+ Egb=Egb*sss_ele_cut
!c! dGGBdR = 0.0d0
!c!-------------------------------------------------------------------
!c! Fisocav - isotropic cavity creation term
FisoCav = top / bot
dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
dbot = 12.0d0 * al4 * pom ** 11.0d0
- dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+ dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut+FisoCav*sss_ele_grad
+ FisoCav=FisoCav*sss_ele_cut
+
!c! dGCVdR = 0.0d0
!c!-------------------------------------------------------------------
!c! Polarization energy
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* ( 2.0d0 - 0.5d0 * ee2) ) &
/ ( 2.0d0 * fgb2 )
- dPOLdR1 = dPOLdFGB1 * dFGBdR1
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut
!c! dPOLdR1 = 0.0d0
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head &
* (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+ (epol+Elj)*sss_ele_grad
+ Elj=Elj*sss_ele_cut
+ epol=epol*sss_ele_cut
!c! dGLJdR = 0.0d0
!c!-------------------------------------------------------------------
!c! Equad
Equad = fac * Beta1
!c! Equad = 0.0d0
!c! derivative of Equad...
- dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
+ dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR*sss_ele_cut&
+ + Equad*sss_ele_grad
+ Equad=Equad*sss_ele_cut
!c! dQUADdR = 0.0d0
dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
!c! dQUADdOM1 = 0.0d0
DO k = 1, 3
dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
- tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
+ tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)*sss_ele_cut
END DO
!c! Radial stuff
DO k = 1, 3
- dQUADdR * pom&
- tuna(k) &
+ (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
- + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+ + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut
pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
!c! this acts on hydrophobic center of interaction
+ dQUADdR * pom &
+ tuna(k) &
+ (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
- + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+ + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut
!c! this acts on Calpha
gheadtail(k,3,1) = gheadtail(k,3,1) &
dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
* (2.0d0 - 0.5d0 * ee1) ) &
/ (2.0d0 * fgb1)
- dPOLdR1 = dPOLdFGB1 * dFGBdR1
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
+ epol=epol*sss_ele_cut
!c! dPOLdR1 = 0.0d0
dPOLdOM1 = 0.0d0
dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+ epol=epol*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+ epol=epol*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
hawk = w2 * Qi * Qi * (1.0d0 - sqom2)
Ecl = sparrow / Rhead**2.0d0 &
- hawk / Rhead**4.0d0
- dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 &
- + 4.0d0 * hawk / Rhead**5.0d0
+ dGCLdR = (- 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut+Ecl*sss_ele_grad
+ Ecl=Ecl*sss_ele_cut
!c! dF/dom1
dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
!c! dF/dom2
dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
* (2.0d0 - 0.5d0 * ee1) ) &
/ (2.0d0 * fgb1)
- dPOLdR1 = dPOLdFGB1 * dFGBdR1
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
!c! dPOLdR1 = 0.0d0
dPOLdOM1 = 0.0d0
dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head &
* (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+elj*sss_ele_grad
+ Elj=Elj*sss_ele_cut
DO k = 1, 3
erhead(k) = Rhead_distance(k)/Rhead
erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
END DO
RETURN
END SUBROUTINE eqd
+
+ SUBROUTINE eqd_cat(Ecl,Elj,Epol)
+ use calc_data
+ use comm_momo
+ double precision facd4, federmaus,ecl,elj,epol
+ alphapol1 = alphapolcat(itypi,itypj)
+ w1 = wqdipcat(1,itypi,itypj)
+ w2 = wqdipcat(2,itypi,itypj)
+ pis = sig0headcat(itypi,itypj)
+ eps_head = epsheadcat(itypi,itypj)
+! eps_head=0.0d0
+! w2=0.0d0
+! alphapol1=0.0d0
+!c!-------------------------------------------------------------------
+!c! R1 - distance between head of ith side chain and tail of jth sidechain
+ R1 = 0.0d0
+ DO k = 1, 3
+!c! Calculate head-to-tail distances
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ END DO
+!c! Pitagoras
+ R1 = dsqrt(R1)
+
+!c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+!c! & +dhead(1,1,itypi,itypj))**2))
+!c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+!c! & +dhead(2,1,itypi,itypj))**2))
+
+!c!-------------------------------------------------------------------
+!c! ecl
+ sparrow = w1 * Qi * om1
+ hawk = w2 * Qi * Qi * (1.0d0 - sqom2)
+ Ecl = sparrow / Rhead**2.0d0 &
+ - hawk / Rhead**4.0d0
+ dGCLdR =sss_ele_cut*(-2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)+sss_ele_grad*ECL
+ ECL=ECL*sss_ele_cut
+!c! dF/dom1
+ dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+!c! dF/dom2
+ dGCLdOM2 = 0.0d0 !
+
+!(2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+
+!c--------------------------------------------------------------------
+!c Polarization energy
+!c Epol
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ RR1 = R1 * R1 / MomoFac1
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1)
+ epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
+!c! epol = 0.0d0
+!c!------------------------------------------------------------------
+!c! derivative of Epol is Gpol...
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
+ / (fgb1 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1) &
+ * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+ / ( 2.0d0 * fgb1 )
+ dFGBdOM2 = 0.0d0 ! as om2 is 0
+! (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
+! * (2.0d0 - 0.5d0 * ee1) ) &
+! / (2.0d0 * fgb1)
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
+!c! dPOLdR1 = 0.0d0
+ dPOLdOM1 = 0.0d0
+! dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+ dPOLdOM2 = 0.0d0
+ epol=epol*sss_ele_cut
+!c!-------------------------------------------------------------------
+!c! Elj
+ pom = (pis / Rhead)**6.0d0
+ Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+!c! derivative of Elj is Glj
+ dGLJdR = 4.0d0 * eps_head*sss_ele_cut &
+ * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad
+ Elj=Elj*sss_ele_cut
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ END DO
+
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+
+ DO k = 1, 3
+ hawk = (erhead_tail(k,1) + &
+ facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gradpepcatx(k,i) = gradpepcatx(k,i) &
+ - dGCLdR * pom&
+ - dPOLdR1 * hawk &
+ - dGLJdR * pom
+
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepcatx(k,j) = gradpepcatx(k,j) &
+! + dGCLdR * pom &
+! + dPOLdR1 * (erhead_tail(k,1) &
+! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
+! + dGLJdR * pom
+
+
+ gradpepcat(k,i) = gradpepcat(k,i) &
+ - dGCLdR * erhead(k) &
+ - dPOLdR1 * erhead_tail(k,1) &
+ - dGLJdR * erhead(k)
+
+ gradpepcat(k,j) = gradpepcat(k,j) &
+ + dGCLdR * erhead(k) &
+ + dPOLdR1 * erhead_tail(k,1) &
+ + dGLJdR * erhead(k)
+
+ END DO
+ RETURN
+ END SUBROUTINE eqd_cat
+
SUBROUTINE edq(Ecl,Elj,Epol)
! IMPLICIT NONE
use comm_momo
!c!-------------------------------------------------------------------
!c! derivative of ecl is Gcl
!c! dF/dr part
- dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 &
- + 4.0d0 * hawk / Rhead**5.0d0
+ dGCLdR =sss_ele_cut*(- 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)+Ecl*sss_ele_grad
!c! dF/dom1
dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
!c! dF/dom2
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
+ epol=epol*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head &
* (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+Elj*sss_ele_grad
+ elj=elj*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c! (see comments in Eqq)
!c!-------------------------------------------------------------------
!c! derivative of ecl is Gcl
!c! dF/dr part
- dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 &
- + 4.0d0 * hawk / Rhead**5.0d0
+ dGCLdR =( - 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut+ECL*sss_ele_grad
!c! dF/dom1
dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
!c! dF/dom2
dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
+ ECL=ECL*sss_ele_cut
!c--------------------------------------------------------------------
!c--------------------------------------------------------------------
!c Polarization energy
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
dPOLdOM2 = 0.0d0
+ epol=epol*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Elj
pom = (pis / Rhead)**6.0d0
!c! derivative of Elj is Glj
dGLJdR = 4.0d0 * eps_head &
* (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+ Elj*sss_ele_grad
+ Elj=Elj*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c!-------------------------------------------------------------------
!c! derivative of ecl is Gcl
!c! dF/dr part
- dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 &
- + 4.0d0 * hawk / Rhead**5.0d0
+ dGCLdR = (- 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut+&
+ ECL*sss_ele_grad
+ ECL=ECL*sss_ele_cut
!c! dF/dom1
dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
!c! dF/dom2
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+ epol=epol*sss_ele_grad
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
pom = (pis / Rhead)**6.0d0
Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
!c! derivative of Elj is Glj
- dGLJdR = 4.0d0 * eps_head &
+ dGLJdR = 4.0d0 * eps_head*sss_ele_cut &
* (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
- + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad
+ Elj=Elj*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
* (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
- dGCLdR = c1 - c2
+ dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+ ECL=ECL*sss_ele_cut
!c! dECL/dom1
c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
END DO
RETURN
END SUBROUTINE edd
+ SUBROUTINE edd_cat(ECL)
+! IMPLICIT NONE
+ use comm_momo
+ use calc_data
+
+ double precision ecl
+!c! csig = sigiso(itypi,itypj)
+ w1 = wqdipcat(1,itypi,itypj)
+ w2 = wqdipcat(2,itypi,itypj)
+! w2=0.0d0
+!c!-------------------------------------------------------------------
+!c! ECL
+! print *,"om1",om1,om2,om12
+ fac = - 3.0d0 * om1 !after integer and simplify
+ c1 = (w1 / (Rhead**3.0d0)) * fac
+ c2 = (w2 / Rhead ** 6.0d0) &
+ * (4.0d0 + 6.0d0*sqom1 ) !after integration and simplification
+ ECL = c1 - c2
+!c! dervative of ECL is GCL...
+!c! dECL/dr
+ c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
+ * (4.0d0 + 6.0d0*sqom1)
+ dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+!c! dECL/dom1
+ c1 = (-3.0d0 * w1) / (Rhead**3.0d0)
+ c2 = (12.0d0 * w2*om1) / (Rhead**6.0d0)
+ dGCLdOM1 = c1 - c2
+!c! dECL/dom2
+! c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
+ c1=0.0 ! this is because om2 is 0
+! c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+! * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+ c2=0.0 !om is 0
+ dGCLdOM2 = c1 - c2
+!c! dECL/dom12
+! c1 = w1 / (Rhead ** 3.0d0)
+ c1=0.0d0 ! this is because om12 is 0
+! c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0
+ c2=0.0d0 !om12 is 0
+ dGCLdOM12 = c1 - c2
+!c!-------------------------------------------------------------------
+!c! Return the results
+!c! (see comments in Eqq)
+ DO k= 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j+nres)
+ DO k = 1, 3
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gradpepcatx(k,i) = gradpepcatx(k,i) - dGCLdR * pom
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepcatx(k,j) = gradpepcatx(k,j) + dGCLdR * pom
+
+ gradpepcat(k,i) = gradpepcat(k,i) - dGCLdR * erhead(k)
+ gradpepcat(k,j) = gradpepcat(k,j) + dGCLdR * erhead(k)
+ END DO
+ RETURN
+ END SUBROUTINE edd_cat
+ SUBROUTINE edd_cat_pep(ECL)
+! IMPLICIT NONE
+ use comm_momo
+ use calc_data
+
+ double precision ecl
+!c! csig = sigiso(itypi,itypj)
+ w1 = wqdipcat(1,itypi,itypj)
+ w2 = wqdipcat(2,itypi,itypj)
+!c!-------------------------------------------------------------------
+!c! ECL
+ fac = (om12 - 3.0d0 * om1 * om2)
+ c1 = (w1 / (Rhead**3.0d0)) * fac
+ c2 = (w2 / Rhead ** 6.0d0) &
+ * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+ ECL = c1 - c2
+!c! dECL/dr
+ c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
+ * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+ dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+ ECL=ECL*sss_ele_cut
+!c! dECL/dom1
+ c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+ * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+ dGCLdOM1 = c1 - c2
+!c! dECL/dom2
+ c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
+ c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+ * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+ dGCLdOM2 = c1 - c2
+ dGCLdOM2=0.0d0 ! this is because om2=0
+!c! dECL/dom12
+ c1 = w1 / (Rhead ** 3.0d0)
+ c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0
+ dGCLdOM12 = c1 - c2
+ dGCLdOM12=0.0d0 !this is because om12=0.0
+!c!-------------------------------------------------------------------
+!c! Return the results
+!c! (see comments in Eqq)
+ DO k= 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i) )
+ erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+ facd1 = d1 * vbld_inv(i)
+ facd2 = d2 * vbld_inv(j+nres)
+ DO k = 1, 3
+
+ pom = facd1*(erhead(k)-erdxi*dC_norm(k,i))
+ gradpepcat(k,i) = gradpepcat(k,i) + dGCLdR * pom
+ gradpepcat(k,i+1) = gradpepcat(k,i+1) - dGCLdR * pom
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepcatx(k,j) = gradpepcatx(k,j) + dGCLdR * pom
+
+ gradpepcat(k,i) = gradpepcat(k,i) - dGCLdR * erhead(k)*0.5d0
+ gradpepcat(k,i+1) = gradpepcat(k,i+1)- dGCLdR * erhead(k)*0.5d0
+ gradpepcat(k,j) = gradpepcat(k,j) + dGCLdR * erhead(k)
+ END DO
+ RETURN
+ END SUBROUTINE edd_cat_pep
+
SUBROUTINE elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
! IMPLICIT NONE
use comm_momo
if (itype(j,5).le.5) then
ilist_catscnorm=ilist_catscnorm+1
! this can be substituted by cantor and anti-cantor
+! write(iout,*) "have contact",i,j,ilist_catscnorm
contlistcatscnormi(ilist_catscnorm)=i
contlistcatscnormj(ilist_catscnorm)=j
+! write(iout,*) "have contact2",i,j,ilist_catscnorm,&
+! contlistcatscnormi(ilist_catscnorm),contlistcatscnormj(ilist_catscnorm)
+
else
ilist_catsctran=ilist_catsctran+1
! this can be substituted by cantor and anti-cantor
ilist_catscnorm,ilist_catpnorm,ilist_catscang
do i=1,ilist_catsctran
- write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i)
+ write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i),&
+ itype(j,contlistcatsctranj(i))
enddo
do i=1,ilist_catptran
write (iout,*) i,contlistcatptrani(i),contlistcatsctranj(i)
enddo
do i=1,ilist_catscnorm
- write (iout,*) i,contlistcatscnormi(i),contlistcatsctranj(i)
+ write (iout,*) i,contlistcatscnormi(i),contlistcatscnormj(i)
enddo
do i=1,ilist_catpnorm
- write (iout,*) i,contlistcatpnormi(i),contlistcatsctranj(i)
+ write (iout,*) i,contlistcatpnormi(i),contlistcatscnormj(i)
enddo
do i=1,ilist_catscang
write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i)
i_ilist_catpnorm(0:nprocs),i_ilist_catsctran(0:nprocs),&
i_ilist_catptran(0:nprocs),i_ilist_catscang(0:nprocs),&
i_ilist_catscangf(0:nprocs),i_ilist_catscangt(0:nprocs)
- write(iout,*),"START make_catcat"
+! write(iout,*),"START make_catcat"
ilist_catpnorm=0
ilist_catscnorm=0
ilist_catptran=0
write (iout,*) i,newcontlistcatcatnormi(i),newcontlistcatcatnormj(i)
enddo
#endif
- write(iout,*),"END make_catcat"
+! write(iout,*),"END make_catcat"
return
end subroutine make_cat_cat_list
boxx(1)=boxxsize
boxx(2)=boxysize
boxx(3)=boxzsize
+ write(iout,*) "start ecattran",g_listcatsctran_start,g_listcatsctran_end
do k=g_listcatsctran_start,g_listcatsctran_end
i=newcontlistcatsctrani(k)
j=newcontlistcatsctranj(k)
!c & itype(chain_border(1,i)+k).eq.itype(chain_border(1,j)+k))
do k=0,chain_length(i)-1
!c k=k+1
- mnum=molnum(k)
+ mnum=molnum(k+1)
if (itype(chain_border(1,i)+k,mnum).ne.&
itype(chain_border(1,j)+k,mnum)) exit
enddo
read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
print *,msc(i,5),restok(i,5)
enddo
- ip(5)=0.2
+! ip(5)=0.2
! isc(5)=0.2
read (iion,*) ncatprotparm
allocate(catprm(ncatprotparm,4))
!HERE THE MASS of MARTINI
write(*,*) "before MARTINI PARAM"
do i=1,ntyp_molec(4)
- msc(i,4)=0.0d0
- mp(4)=72.0d0
+ msc(i,4)=72.0d0
+ mp(4)=0.0d0
isc(i,4)=0.d0
enddo
ip(4)=0.0
+ msc(ntyp_molec(4)+1,4)=0.1d0
!relative dielectric constant = 15 for implicit screening
k_coulomb_lip=332.0d0/15.0d0
!kbond = 1250 kJ/(mol*nm*2)
! Ions by Aga
- allocate(alphapolcat(ntyp,ntyp),epsheadcat(ntyp,ntyp),sig0headcat(ntyp,ntyp))
- allocate(alphapolcat2(ntyp,ntyp))
- allocate(sigiso1cat(ntyp,ntyp),rborn1cat(ntyp,ntyp),rborn2cat(ntyp,ntyp),sigmap1cat(ntyp,ntyp))
- allocate(sigmap2cat(ntyp,ntyp),sigiso2cat(ntyp,ntyp))
- allocate(chis1cat(ntyp,ntyp),chis2cat(ntyp,ntyp),wquadcat(ntyp,ntyp),chipp1cat(ntyp,ntyp),chipp2cat(ntyp,ntyp))
- allocate(epsintabcat(ntyp,ntyp))
- allocate(dtailcat(2,ntyp,ntyp))
- allocate(alphasurcat(4,ntyp,ntyp),alphisocat(4,ntyp,ntyp))
- allocate(wqdipcat(2,ntyp,ntyp))
- allocate(wstatecat(4,ntyp,ntyp))
- allocate(dheadcat(2,2,ntyp,ntyp))
- allocate(nstatecat(ntyp,ntyp))
- allocate(debaykapcat(ntyp,ntyp))
-
- if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,0:ntyp1))
- if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
+ allocate(alphapolcat(ntyp,-1:ntyp_molec(5)),epsheadcat(ntyp,-1:ntyp_molec(5)),sig0headcat(ntyp,-1:ntyp_molec(5)))
+ allocate(alphapolcat2(ntyp,-1:ntyp_molec(5)))
+ allocate(sigiso1cat(ntyp,-1:ntyp_molec(5)),rborn1cat(ntyp,-1:ntyp_molec(5)),rborn2cat(ntyp,-1:ntyp_molec(5)),sigmap1cat(ntyp,-1:ntyp_molec(5)))
+ allocate(sigmap2cat(ntyp,-1:ntyp_molec(5)),sigiso2cat(ntyp,-1:ntyp_molec(5)))
+ allocate(chis1cat(ntyp,-1:ntyp_molec(5)),chis2cat(ntyp,-1:ntyp_molec(5)),wquadcat(ntyp,-1:ntyp_molec(5)),chipp1cat(ntyp,-1:ntyp_molec(5)),chipp2cat(ntyp,-1:ntyp_molec(5)))
+ allocate(epsintabcat(ntyp,-1:ntyp_molec(5)))
+ allocate(dtailcat(2,ntyp,-1:ntyp_molec(5)))
+ allocate(alphasurcat(4,ntyp,-1:ntyp_molec(5)),alphisocat(4,ntyp,-1:ntyp_molec(5)))
+ allocate(wqdipcat(2,ntyp,-1:ntyp_molec(5)))
+ allocate(wstatecat(4,ntyp,-1:ntyp_molec(5)))
+ allocate(dheadcat(2,2,ntyp,-1:ntyp_molec(5)))
+ allocate(nstatecat(ntyp,-1:ntyp_molec(5)))
+ allocate(debaykapcat(ntyp,-1:ntyp_molec(5)))
+
+ if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,-1:ntyp1))
+ if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,-1:ntyp1))
! if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
- if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,ntyp1)) !(ntyp,ntyp)
- if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)
if (.not.allocated(ichargecat))&
! mp(5)=0.2
pstok(5)=3.0
!DIR$ NOUNROLL
- do j=1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+ do j=-1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+ if (j.eq.0) cycle
do i=1,ntyp
! do j=1,ntyp_molec(5)
! write (*,*) "Im in ALAB", i, " ", j
read(iion,*) &
epscat(i,j),sigmacat(i,j), &
! chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
- chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), &
+ chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), & !6
- (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
+ (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&!12
! chiscat(i,j),chiscat(j,i), &
chis1cat(i,j),chis2cat(i,j), &
- nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !5 w tej lini - 1 integer pierwszy
- dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
+ nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !19 !5 w tej lini - 1 integer pierwszy
+ dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&!23
dtailcat(1,i,j),dtailcat(2,i,j), &
- epsheadcat(i,j),sig0headcat(i,j), &
+ epsheadcat(i,j),sig0headcat(i,j), &!27
!wdipcat = w1 , w2
! rborncat(i,j),rborncat(j,i),&
rborn1cat(i,j),rborn2cat(i,j),&
- (wqdipcat(k,i,j),k=1,2), &
- alphapolcat(i,j),alphapolcat2(j,i), &
+ (wqdipcat(k,i,j),k=1,2), &!31
+ alphapolcat(i,j),alphapolcat2(j,i), &!33
(alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
if (chi1cat(i,j).gt.0.9) write (*,*) "WTF ANISO", i,j, chi1cat(i,j)
END DO
END DO
- allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
+ allocate(aa_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)),&
+ bb_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)))
do i=1,ntyp
- do j=1,ntyp_molec(5)
+ do j=-1,ntyp_molec(5)
+ if (j.eq.0) cycle
epsij=epscat(i,j)
rrij=sigmacat(i,j)
rrij=rrij**expon
call exec_softreg
else if (modecalc.eq.12) then
call exec_MD
-! call exec_checkgrad
+ call exec_checkgrad
else if (modecalc.eq.14) then
call exec_MREMD
else
projects / unres4.git / commitdiff