!el external ilen
character(len=50) :: tytul
!el common /gucio/ cm
- integer :: itime,i,j,nharp
+ integer :: i,j,nharp
integer,dimension(4,nres/3) :: iharp !(4,nres/3)(4,maxres/3)
! logical :: ovrtim
real(kind=8) :: tt0,scalfac
- integer :: nres2
+ integer :: nres2,itime
nres2=2*nres
print *, "ENTER MD"
!
stop
#endif
endif
+ itime_mat=itime
if (ntwe.ne.0) then
if (mod(itime,ntwe).eq.0) then
call statout(itime)
!el common /gucio/ cm
!el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
!el common /stochcalc/ stochforcvec
- integer :: itime,icount_scale,itime_scal,i,j,ifac_time,iretcode
+ integer :: icount_scale,itime_scal,i,j,ifac_time,iretcode,itime
logical :: scalel
real(kind=8) :: epdrift,tt0,fac_time
!
call etotal(potEcomp)
! AL 4/17/17: Reduce the steps if NaNs occurred.
if (potEcomp(0).gt.0.99e18 .or. isnan(potEcomp(0)).gt.0) then
+ call enerprint(potEcomp)
d_time=d_time/10.0
if (icount_scale.gt.15) then
write (iout,*) "Tu jest problem",potEcomp(0),d_time
!el common /gucio/ cm
!el real(kind=8),dimension(6*nres) :: stochforcvec !(MAXRES6) maxres6=6*maxres
!el common /stochcalc/ stochforcvec
- integer :: itime,itt,i,j,itsplit
+ integer :: itt,i,j,itsplit,itime
logical :: scale
!el common /cipiszcze/ itt
character(len=50) :: tytul
logical :: file_exist
!el common /gucio/ cm
- integer :: i,j,ipos,iq,iw,nft_sc,iretcode,nfun,itime,ierr,mnum
+ integer :: i,j,ipos,iq,iw,nft_sc,iretcode,nfun,ierr,mnum,itime
real(kind=8) :: etot,tt0
logical :: fail
potE=potEcomp(0)-potEcomp(20)
totE=EK+potE
itime=0
+ itime_mat=itime
if (ntwe.ne.0) call statout(itime)
if(me.eq.king.or..not.out1file) &
write (iout,'(/a/3(a25,1pe14.5/))') "Initial:", &
real(kind=8) :: remd_t_bath(Nprocs) !(maxprocs)
integer :: iremd_iset(Nprocs) !(maxprocs)
- integer(kind=2) :: i_index(Nprocs,Nprocs,Nprocs,Nprocs)
+ integer(kind=2) :: i_index(Nprocs/2,Nprocs/2,Nprocs/10,Nprocs/10)
! (maxprocs/4,maxprocs/20,maxprocs/200,maxprocs/200)
real(kind=8) :: remd_ene(0:n_ene+4,Nprocs) !(0:n_ene+4,maxprocs)
integer :: iremd_acc(Nprocs),iremd_tot(Nprocs) !(maxprocs)
!el external ilen
character(len=50) :: tytul
!el common /gucio/ cm
- integer :: itime
+! integer :: itime
!old integer nup(0:maxprocs),ndown(0:maxprocs)
integer :: rep2i(0:Nprocs),ireqi(Nprocs) !(maxprocs)
integer :: icache_all(Nprocs) !(maxprocs)
econstr_temp_iex
integer :: k,il,il1,i,j,nharp,ii,ierr,itime_master,irr,iex,&
i_set_temp,itmp,i_temp,i_mult,i_iset,i_mset,i_dir,i_temp1,&
- i_mult1,i_iset1,i_mset1,ierror
+ i_mult1,i_iset1,i_mset1,ierror,itime
integer,dimension(4,nres/3) :: iharp !(4,nres/3)(4,maxres/3)
!deb imin_itime_old=0
integer :: nres2 !el
tt0=tcpu()
#endif
itime=0
+ itime_mat=itime
end_of_run=.false.
do while(.not.end_of_run)
itime=itime+1
+ itime_mat=itime
if(itime.eq.n_timestep.and.me.eq.king) end_of_run=.true.
if(mremdsync.and.itime.eq.n_timestep) end_of_run=.true.
rstcount=rstcount+1
stop
#endif
endif
+ itime_mat=itime
if(ntwe.ne.0) then
if (mod(itime,ntwe).eq.0) then
call statout(itime)
! common /back_constr/ in module.energy
! common /qmeas/ others in module.geometry
real(kind=8) :: eq_time
- integer :: iset,nset
+ integer :: iset,nset,itime_mat
integer,dimension(:),allocatable :: mset !(maxprocs/20)
logical :: usampl
! common /mdpar/
! include 'COMMON.TIME1'
real(kind=8) :: time00
!el local variables
- integer :: n_corr,n_corr1,ierror
+ integer :: n_corr,n_corr1,ierror,imatupdate
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,eliptran,etube, &
integer ishield_listbuf(-1:nres), &
shield_listbuf(maxcontsshi,-1:nres),k,j,i,iii,impishi,mojint,jjj
-
-
+! print *,"I START ENERGY"
+ imatupdate=1
+! if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
! real(kind=8), dimension(:),allocatable:: fac_shieldbuf
! real(kind=8), dimension(:,:,:),allocatable:: &
! grad_shield_locbuf,grad_shield_sidebuf
time_Bcastw=time_Bcastw+MPI_Wtime()-time00
! call chainbuild_cart
endif
+! if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
+
! print *,'Processor',myrank,' calling etotal ipot=',ipot
! print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
#else
eespp=0.0d0
endif
! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
-! print *,"before ecatcat",wcatcat
+ print *,"before ecatcat",wcatcat
if (nfgtasks.gt.1) then
if (fg_rank.eq.0) then
call ecatcat(ecationcation)
enddo
#endif
!#undef DEBUG
- do i=1,nres
+ do i=0,nres
do j=1,3
gloc_scbuf(j,i)=gloc_sc(j,i,icg)
enddo
call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,&
MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
- call MPI_Reduce(gloc_scbuf(1,1),gloc_sc(1,1,icg),3*nres,&
+ call MPI_Reduce(gloc_scbuf(1,0),gloc_sc(1,0,icg),3*nres+3,&
MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
time_reduce=time_reduce+MPI_Wtime()-time00
!#define DEBUG
! print *,"gradbuf",gradbufc(1,1),gradc(1,1,icg)
#ifdef DEBUG
write (iout,*) "gloc_sc after reduce"
- do i=1,nres
+ do i=0,nres
do j=1,1
write (iout,*) i,j,gloc_sc(j,i,icg)
enddo
!#define DEBUG
!el write (iout,*) "After sum_gradient"
#ifdef DEBUG
-!el write (iout,*) "After sum_gradient"
+ write (iout,*) "After sum_gradient"
do i=1,nres-1
write (iout,*) i," gradc ",(gradc(j,i,icg),j=1,3)
write (iout,*) i," gradx ",(gradx(j,i,icg),j=1,3)
dphi(j,1,i)=0.0d0
dphi(j,2,i)=0.0d0
dphi(j,3,i)=0.0d0
+ dcosomicron(j,1,1,i)=0.0d0
+ dcosomicron(j,1,2,i)=0.0d0
+ dcosomicron(j,2,1,i)=0.0d0
+ dcosomicron(j,2,2,i)=0.0d0
enddo
enddo
! Derivatives of theta's
#else
do i=3,nres
#endif
- if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1)) then
+ if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1).and.molnum(i).ne.5) then
cost1=dcos(omicron(1,i))
sint1=sqrt(1-cost1*cost1)
cost2=dcos(omicron(2,i))
xi=c(1,i)
yi=c(2,i)
zi=c(3,i)
+! write (iout,*) i,"TUTUT",c(1,i)
itypi=itype(i,5)
xi=mod(xi,boxxsize)
if (xi.lt.0) xi=xi+boxxsize
do j=i+1,itmp+nres_molec(5)
itypj=itype(j,5)
+! print *,i,j,itypi,itypj
k0 = 332.0*(ichargecat(itypi)*ichargecat(itypj))/80.0
! print *,i,j,'catcat'
xj=c(1,j)
do i=1,4
itmp=itmp+nres_molec(i)
enddo
- go to 17
+! go to 17
! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization
do i=ibond_start,ibond_end
! tail location and distance calculations
! dhead1
d1 = dheadcat(1, 1, itypi, itypj)
+! print *,"d1",d1
+! d1=0.0d0
! d2 = dhead(2, 1, itypi, itypj)
DO k = 1,3
! location of polar head is computed by taking hydrophobic centre
- 2.0d0 * chis12 * om1 * om2 * om12
pom = 1.0d0 - chis1 * chis2 * sqom12
- print *,"TUT2",fac,chis1,sqom1,pom
+! print *,"TUT2",fac,chis1,sqom1,pom
Lambf = (1.0d0 - (fac / pom))
Lambf = dsqrt(Lambf)
sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
CALL edq_cat_pep(ecl, elj, epol)
eheadtail = ECL + elj + epol
! print *,"i,",i,eheadtail
- eheadtail = 0.0d0
+! eheadtail = 0.0d0
evdw = evdw + Fcav + eheadtail
!c! ecl
sparrow = w1 * Qj * om1
hawk = w2 * Qj * Qj * (1.0d0 - sqom2)
+! print *,"CO2", itypi,itypj
! print *,"CO?!.", w1,w2,Qj,om1
ECL = sparrow / Rhead**2.0d0 &
- hawk / Rhead**4.0d0
erhead(k) = Rhead_distance(k)/Rhead
erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
END DO
- erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxi = scalar( erhead(1), dC_norm(1,i) )
erdxj = scalar( erhead(1), dC_norm(1,j) )
eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
- adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i) )
facd1 = d1 * vbld_inv(i+1)/2.0
facd2 = d2 * vbld_inv(j)
- facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+nres)
+ facd3 = dtailcat(1,itypi,itypj) * vbld_inv(i+1)/2.0
DO k = 1, 3
condor = (erhead_tail(k,2) &
+ facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
- pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i))
! gradpepcatx(k,i) = gradpepcatx(k,i) &
! - dGCLdR * pom &
! - dPOLdR2 * (erhead_tail(k,2) &
return
end function gradtschebyshev
+ subroutine make_SCSC_inter_list
+ include 'mpif.h'
+ real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+ real*8 :: dist_init, dist_temp,r_buff_list
+ integer:: contlisti(50*nres),contlistj(50*nres)
+ integer :: newcontlisti(50*nres),newcontlistj(50*nres)
+ integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_sc,g_ilist_sc
+ integer displ(0:nprocs),i_ilist_sc(0:nprocs),ierr
+! print *,"START make_SC"
+ ilist_sc=0
+ do i=iatsc_s,iatsc_e
+ itypi=iabs(itype(i,1))
+ if (itypi.eq.ntyp1) cycle
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ xi=dmod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=dmod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=dmod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+ do iint=1,nint_gr(i)
+ do j=istart(i,iint),iend(i,iint)
+ itypj=iabs(itype(j,1))
+ if (itypj.eq.ntyp1) cycle
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ xj=dmod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=dmod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=dmod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+! r_buff_list is a read value for a buffer
+ if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+ ilist_sc=ilist_sc+1
+! this can be substituted by cantor and anti-cantor
+ contlisti(ilist_sc)=i
+ contlistj(ilist_sc)=j
+
+ endif
+ enddo
+ enddo
+ enddo
+! call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
+! MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+! call MPI_Gather(newnss,1,MPI_INTEGER,&
+! i_newnss,1,MPI_INTEGER,king,FG_COMM,IERR)
+#ifdef DEBUG
+ write (iout,*) "before MPIREDUCE",ilist_sc
+ do i=1,ilist_sc
+ write (iout,*) i,contlisti(i),contlistj(i)
+ enddo
+#endif
+ if (nfgtasks.gt.1)then
+
+ call MPI_Reduce(ilist_sc,g_ilist_sc,1,&
+ MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+ call MPI_Gather(ilist_sc,1,MPI_INTEGER,&
+ i_ilist_sc,1,MPI_INTEGER,king,FG_COMM,IERR)
+ displ(0)=0
+ do i=1,nfgtasks-1,1
+ displ(i)=i_ilist_sc(i-1)+displ(i-1)
+ enddo
+! write(iout,*) "before gather",displ(0),displ(1)
+ call MPI_Gatherv(contlisti,ilist_sc,MPI_INTEGER,&
+ newcontlisti,i_ilist_sc,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Gatherv(contlistj,ilist_sc,MPI_INTEGER,&
+ newcontlistj,i_ilist_sc,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+ call MPI_Bcast(newcontlisti,g_ilist_sc,MPI_INT,king,FG_COMM,IERR)
+ call MPI_Bcast(newcontlistj,g_ilist_sc,MPI_INT,king,FG_COMM,IERR)
+
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+
+ else
+ g_ilist_sc=ilist_sc
+
+ do i=1,ilist_sc
+ newcontlisti(i)=contlisti(i)
+ newcontlistj(i)=contlistj(i)
+ enddo
+ endif
+
+#ifdef DEBUG
+ write (iout,*) "after MPIREDUCE",g_ilist_sc
+ do i=1,g_ilist_sc
+ write (iout,*) i,newcontlisti(i),newcontlistj(i)
+ enddo
+#endif
+
+ return
+ end subroutine make_SCSC_inter_list
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+ subroutine make_SCp_inter_list
+ include 'mpif.h'
+ real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+ real*8 :: dist_init, dist_temp,r_buff_list
+ integer:: contlistscpi(50*nres),contlistscpj(50*nres)
+ integer :: newcontlistscpi(50*nres),newcontlistscpj(50*nres)
+ integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_scp,g_ilist_scp
+ integer displ(0:nprocs),i_ilist_scp(0:nprocs),ierr
+ print *,"START make_SC"
+ ilist_scp=0
+ do i=iatscp_s,iatscp_e
+ if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle
+ xi=0.5D0*(c(1,i)+c(1,i+1))
+ yi=0.5D0*(c(2,i)+c(2,i+1))
+ zi=0.5D0*(c(3,i)+c(3,i+1))
+ xi=mod(xi,boxxsize)
+ if (xi.lt.0) xi=xi+boxxsize
+ yi=mod(yi,boxysize)
+ if (yi.lt.0) yi=yi+boxysize
+ zi=mod(zi,boxzsize)
+ if (zi.lt.0) zi=zi+boxzsize
+ do iint=1,nscp_gr(i)
+ do j=iscpstart(i,iint),iscpend(i,iint)
+ itypj=iabs(itype(j,1))
+ if (itypj.eq.ntyp1) cycle
+! Uncomment following three lines for SC-p interactions
+! xj=c(1,nres+j)-xi
+! yj=c(2,nres+j)-yi
+! zj=c(3,nres+j)-zi
+! Uncomment following three lines for Ca-p interactions
+! xj=c(1,j)-xi
+! yj=c(2,j)-yi
+! zj=c(3,j)-zi
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ xj=mod(xj,boxxsize)
+ if (xj.lt.0) xj=xj+boxxsize
+ yj=mod(yj,boxysize)
+ if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+! r_buff_list is a read value for a buffer
+ if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+ ilist_scp=ilist_scp+1
+! this can be substituted by cantor and anti-cantor
+ contlistscpi(ilist_scp)=i
+ contlistscpj(ilist_scp)=j
+ endif
+ enddo
+ enddo
+ enddo
+#ifdef DEBUG
+ write (iout,*) "before MPIREDUCE",ilist_scp
+ do i=1,ilist_scp
+ write (iout,*) i,contlistscpi(i),contlistscpj(i)
+ enddo
+#endif
+ if (nfgtasks.gt.1)then
+
+ call MPI_Reduce(ilist_scp,g_ilist_scp,1,&
+ MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+ call MPI_Gather(ilist_scp,1,MPI_INTEGER,&
+ i_ilist_scp,1,MPI_INTEGER,king,FG_COMM,IERR)
+ displ(0)=0
+ do i=1,nfgtasks-1,1
+ displ(i)=i_ilist_scp(i-1)+displ(i-1)
+ enddo
+! write(iout,*) "before gather",displ(0),displ(1)
+ call MPI_Gatherv(contlistscpi,ilist_scp,MPI_INTEGER,&
+ newcontlistscpi,i_ilist_scp,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Gatherv(contlistscpj,ilist_scp,MPI_INTEGER,&
+ newcontlistscpj,i_ilist_scp,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Bcast(g_ilist_scp,1,MPI_INT,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+ call MPI_Bcast(newcontlistscpi,g_ilist_scp,MPI_INT,king,FG_COMM,IERR)
+ call MPI_Bcast(newcontlistscpj,g_ilist_scp,MPI_INT,king,FG_COMM,IERR)
+
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+
+ else
+ g_ilist_scp=ilist_scp
+
+ do i=1,ilist_scp
+ newcontlistscpi(i)=contlistscpi(i)
+ newcontlistscpj(i)=contlistscpj(i)
+ enddo
+ endif
+
+#ifdef DEBUG
+ write (iout,*) "after MPIREDUCE",g_ilist_scp
+ do i=1,g_ilist_scp
+ write (iout,*) i,newcontlistscpi(i),newcontlistscpj(i)
+ enddo
+#endif
+ return
+ end subroutine make_SCp_inter_list
+
+!-----------------------------------------------------------------------------
+!-----------------------------------------------------------------------------
end module energy
do j=1,3
gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
+gloc(nres-2,icg)*dtheta(j,1,3)
+! write(iout,*) "pierwszy gcart", gcart(j,2)
if ((itype(2,1).ne.10).and.&
- (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
+ (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)).and.(molnum(2).ne.5))) then
gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
endif
do j=1,3
gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
- if(itype(2,1).ne.10) then
+! write(iout,*) "drugi gcart", gcart(j,2)
+ if((itype(2,1).ne.10).and.(molnum(2).ne.5)) then
gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
endif
! The side-chain vector derivatives
do i=2,nres-1
if(itype(i,1).ne.10 .and. &
- itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
+ itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)).and.&
+ (molnum(i).ne.5)) then
do j=1,3
gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
+gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
! INTERTYP=3 SC...Ca...Ca...SC
! calculating dE/ddc1
18 continue
+! write(iout,*) "przed sccor gcart", gcart(1,2)
+
! do i=1,nres
! gloc(i,icg)=0.0D0
! write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
if (nres.lt.2) return
if ((nres.lt.3).and.(itype(1,1).eq.10)) return
if ((itype(1,1).ne.10).and. &
- (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
+ (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))).and.(molnum(1).ne.5)) then
do j=1,3
!c Derviative was calculated for oposite vector of side chain therefore
! there is "-" sign before gloc_sc
gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
dtauangle(j,1,2,3)
if ((itype(2,1).ne.10).and. &
- (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
+ (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2))).and.(molnum(2).ne.5)) then
gxcart(j,1)= gxcart(j,1) &
-gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
! ommited
! & +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
+! write(iout,*) "przed dE/ddc2 gcart", gcart(1,2)
+
! Calculating the remainder of dE/ddc2
do j=1,3
if((itype(2,1).ne.10).and. &
- (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
+ (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)).and.(molnum(2).ne.5))) then
if ((itype(1,1).ne.10).and.&
- ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
+ ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))).and.(molnum(1).ne.5))&
gxcart(j,2)=gxcart(j,2)+ &
gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
- if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
+ if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3)).and.molnum(3).ne.5) &
then
gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
!c the - above is due to different vector direction
gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
!c the - above is due to different vector direction
gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
-! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
+ write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart",gcart(j,2)
! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
endif
endif
if ((itype(1,1).ne.10).and.&
- (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
+ (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))).and.(molnum(1).ne.5)) then
gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
! write(iout,*) gloc_sc(1,0,icg),dtauangle(j,1,3,3)
endif
- if ((itype(3,1).ne.10).and.(nres.ge.3)) then
+ if ((itype(3,1).ne.10).and.(nres.ge.3).and.(molnum(3).ne.5)) then
gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
! write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
endif
- if ((itype(4,1).ne.10).and.(nres.ge.4)) then
+ if ((itype(4,1).ne.10).and.(nres.ge.4).and.(molnum(4).ne.5)) then
gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
! write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
endif
! write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
enddo
+! write(iout,*) "po dE/ddc2 gcart", gcart(1,2)
+
! If there are more than five residues
if(nres.ge.5) then
do i=3,nres-2
do j=1,3
! write(iout,*) "before", gcart(j,i)
if ((itype(i,1).ne.10).and.&
- (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
+ (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))).and.(molnum(i).ne.5)) then
gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
*dtauangle(j,2,3,i+1) &
-gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
! & gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
! if (itype(i-1,1).ne.10) then
if ((itype(i-1,1).ne.10).and.&
- (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
+ (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1))).and.(molnum(i-1).eq.5)) then
gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
*dtauangle(j,3,3,i+1)
endif
! if (itype(i+2,1).ne.10) then
if ((itype(i+2,1).ne.10).and.&
- (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
+ (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2))).and.(molnum(i+2).ne.5)) then
gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
dtauangle(j,2,1,i+3)
endif
if(nres.ge.4) then
do j=1,3
if ((itype(nres-1,1).ne.10).and.&
- (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
+ (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1))).and.(molnum(nres-1).ne.5)) then
gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
*dtauangle(j,2,3,nres)
! write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
! & dtauangle(j,2,3,nres), gxcart(j,nres-1)
! if (itype(nres-2,1).ne.10) then
if ((itype(nres-2,1).ne.10).and.&
- (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
+ (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2))).and.(molnum(nres-2).ne.5)) then
gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
*dtauangle(j,3,3,nres)
endif
if ((itype(nres,1).ne.10).and.&
- (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
+ (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))).and.(molnum(nres).ne.5)) then
gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
*dtauangle(j,3,1,nres+1)
gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
endif
endif
if ((itype(nres-2,1).ne.10).and.&
- (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
+ (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2))).and.(molnum(nres-2).ne.5)) then
gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
dtauangle(j,1,3,nres)
endif
- if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
+ if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))).and.(molnum(nres).ne.5)) then
gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
dtauangle(j,2,2,nres+1)
! write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
endif
! Settind dE/ddnres
if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
- (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
+ (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))).and.(molnum(nres).ne.5))then
do j=1,3
gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
*dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
*dtauangle(j,2,3,nres+1)
enddo
endif
+! write(iout,*) "final gcart",gcart(1,2)
! The side-chain vector derivatives
! print *,"gcart",gcart(:,:)
return
print *,msc(i,5),restok(i,5)
enddo
ip(5)=0.2
-
+!DIR$ NOUNROLL
do j=1,ntyp_molec(5)
do i=1,ntyp
! do j=1,ntyp_molec(5)
do i=1,ntyp
do j=1,ntyp_molec(5)
- if (i.eq.1) then
+ if (i.eq.10) then
write (iout,*) 'i= ', i, ' j= ', j
write (iout,*) 'epsi0= ', epscat(i,j)
write (iout,*) 'sigma0= ', sigmacat(i,j)
write (iout,*) 'epsin= ', epsintabcat(1,j), epsintabcat(j,1)
write (iout,*) 'alphapol1= ', alphapolcat(1,j)
write (iout,*) 'alphapol2= ', alphapolcat(j,1)
- write (iout,*) 'w1= ', wqdipcat(1,1,j)
- write (iout,*) 'w2= ', wqdipcat(2,1,j)
+ write (iout,*) 'w1= ', wqdipcat(1,i,j)
+ write (iout,*) 'w2= ', wqdipcat(2,i,j)
write (iout,*) 'debaykapcat(i,j)= ', debaykapcat(1,j)
endif
istype(i)=istype_temp(i)
enddo
enddo
+ if ((itype(1,1).eq.ntyp1).and.itype(2,5).ne.0) then
+! I have only ions now dummy atoms in the system
+ molnum(1)=5
+ itype(1,5)=itype(2,5)
+ itype(1,1)=0
+ do i=2,nres
+ itype(i,5)=itype(i+1,5)
+ enddo
+ itype(nres,5)=0
+ nres=nres-1
+ nres_molec(1)=nres_molec(1)-1
+ endif
! if (itype(1,1).eq.ntyp1) then
! nsup=nsup-1
! nstart_sup=2
projects / unres4.git / commitdiff