nbond=nct-nnt
do i=nnt,nct
- if (itype(i).ne.10) nbond=nbond+1
+ if (itype(i,1).ne.10) nbond=nbond+1
enddo
!
if (lprn1) then
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind1=ind1+1
do j=1,3
Bmat(ind+j,ind1)=dC_norm(j,i+nres)
Td(i)=Td(i)+vbl*Tmat(i,ind)
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
ind=ind+1
- Td(i)=Td(i)+vbldsc0(1,itype(k))*Tmat(i,ind)
+ Td(i)=Td(i)+vbldsc0(1,itype(k,1))*Tmat(i,ind)
endif
enddo
enddo
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
do j=1,3
ind=ind+1
zapas(ind)=-gxcart(j,i)+stochforcvec(ind)
i,(dC(j,i),j=1,3),xx
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
- xx=vbld(i+nres)-vbldsc0(1,itype(i))
+ xx=vbld(i+nres)-vbldsc0(1,itype(i,1))
write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
i,(dC(j,i+nres),j=1,3),xx
endif
endif
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
blen2 = scalar(dc(1,i+nres),dc(1,i+nres))
- ppvec(ind)=2*vbldsc0(1,itype(i))**2-blen2
- diffbond=dabs(vbldsc0(1,itype(i))-dsqrt(blen2))
+ ppvec(ind)=2*vbldsc0(1,itype(i,1))**2-blen2
+ diffbond=dabs(vbldsc0(1,itype(i,1))-dsqrt(blen2))
if (diffbond.gt.diffmax) diffmax=diffbond
if (ppvec(ind).gt.0.0d0) then
ppvec(ind)=dsqrt(ppvec(ind))
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
do j=1,3
dc(j,i+nres)=zapas(ind+j)
dc_work(ind+j)=zapas(ind+j)
i,(dC(j,i),j=1,3),xx
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
- xx=vbld(i+nres)-vbldsc0(1,itype(i))
+ xx=vbld(i+nres)-vbldsc0(1,itype(i,1))
write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
i,(dC(j,i+nres),j=1,3),xx
endif
potE=potEcomp(0)-potEcomp(20)
call cartgrad
totT=totT+d_time
+ totTafm=totT
! Calculate the kinetic and total energy and the kinetic temperature
call kinetic(EK)
#ifdef MPI
! include 'COMMON.IOUNITS'
real(kind=8) :: KE_total
- integer :: i,j,k,iti
+ integer :: i,j,k,iti,mnum
real(kind=8) :: KEt_p,KEt_sc,KEr_p,KEr_sc,incr(3),&
mag1,mag2,v(3)
#ifdef DEBUG
#endif
KEt_p=0.0d0
KEt_sc=0.0d0
-! write (iout,*) "ISC",(isc(itype(i)),i=1,nres)
+! write (iout,*) "ISC",(isc(itype(i,1)),i=1,nres)
! The translational part for peptide virtual bonds
do j=1,3
incr(j)=d_t(j,0)
enddo
do i=nnt,nct-1
+ mnum=molnum(i)
! write (iout,*) "Kinetic trp:",i,(incr(j),j=1,3)
do j=1,3
v(j)=incr(j)+0.5d0*d_t(j,i)
enddo
vtot(i)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
- KEt_p=KEt_p+(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
+ KEt_p=KEt_p+mp(mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
do j=1,3
incr(j)=incr(j)+d_t(j,i)
enddo
incr(j)=d_t(j,0)
enddo
do i=nnt,nct
- iti=iabs(itype(i))
- if (itype(i).eq.10) then
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
+ .or.(mnum.eq.5)) then
do j=1,3
v(j)=incr(j)
enddo
endif
! write (iout,*) "Kinetic trsc:",i,(incr(j),j=1,3)
! write (iout,*) "i",i," msc",msc(iti)," v",(v(j),j=1,3)
- KEt_sc=KEt_sc+msc(iti)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
+ KEt_sc=KEt_sc+msc(iti,mnum)*(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
vtot(i+nres)=v(1)*v(1)+v(2)*v(2)+v(3)*v(3)
do j=1,3
incr(j)=incr(j)+d_t(j,i)
! The part due to stretching and rotation of the peptide groups
KEr_p=0.0D0
do i=nnt,nct-1
+ mnum=molnum(i)
! write (iout,*) "i",i
! write (iout,*) "i",i," mag1",mag1," mag2",mag2
do j=1,3
incr(j)=d_t(j,i)
enddo
! write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
- KEr_p=KEr_p+(incr(1)*incr(1)+incr(2)*incr(2) &
+ KEr_p=KEr_p+Ip(mnum)*(incr(1)*incr(1)+incr(2)*incr(2) &
+incr(3)*incr(3))
enddo
! goto 111
! The rotational part of the side chain virtual bond
KEr_sc=0.0D0
do i=nnt,nct
- iti=iabs(itype(i))
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
incr(j)=d_t(j,nres+i)
enddo
! write (iout,*) "Kinetic rotsc:",i,(incr(j),j=1,3)
- KEr_sc=KEr_sc+Isc(iti)*(incr(1)*incr(1)+incr(2)*incr(2)+ &
+ KEr_sc=KEr_sc+Isc(iti,mnum)*(incr(1)*incr(1)+incr(2)*incr(2)+ &
incr(3)*incr(3))
endif
enddo
! The total kinetic energy
111 continue
! write(iout,*) 'KEr_sc', KEr_sc
- KE_total=0.5d0*(mp*KEt_p+KEt_sc+0.25d0*Ip*KEr_p+KEr_sc)
+ KE_total=0.5d0*(KEt_p+KEt_sc+0.25d0*KEr_p+KEr_sc)
! write (iout,*) "KE_total",KE_total
return
end subroutine kinetic
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
do j=1,3
ind=ind+1
v_work(ind)=d_t(j,i+nres)
if (rstcount.eq.1000.or.itime.eq.n_timestep) then
open(irest2,file=rest2name,status='unknown')
write(irest2,*) totT,EK,potE,totE,t_bath
+ totTafm=totT
! AL 4/17/17: Now writing d_t(0,:) too
do i=0,2*nres
write (irest2,'(3e15.5)') (d_t(j,i),j=1,3)
endif
if (rattle) call rattle2
totT=totT+d_time
+ totTafm=totT
if (d_time.ne.d_time0) then
d_time=d_time0
#ifndef LANG0
potE=potEcomp(0)-potEcomp(20)
! potE=energia_short(0)+energia_long(0)
totT=totT+d_time
+ totTafm=totT
! Calculate the kinetic and the total energy and the kinetic temperature
call kinetic(EK)
totE=EK+potE
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- integer :: i,j,inres
+ integer :: i,j,inres,mnum
do j=1,3
d_t(j,0)=d_t(j,0)+0.5d0*d_a(j,0)*d_time
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
real(kind=8) :: adt,adt2
- integer :: i,j,inres
+ integer :: i,j,inres,mnum
#ifdef DEBUG
write (iout,*) "VELVERLET1 START: DC"
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
adt=d_a_old(j,inres)*d_time
! include 'COMMON.INTERACT'
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
- integer :: i,j,inres
+ integer :: i,j,inres,mnum
do j=1,3
d_t(j,0)=d_t_new(j,0)+0.5d0*d_a(j,0)*d_time
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
! position and velocity increments included.
real(kind=8) :: sqrt13 = 0.57735026918962576451d0 ! 1/sqrt(3)
real(kind=8) :: adt,adt2
- integer :: i,j,ind,inres
+ integer :: i,j,ind,inres,mnum
!
! Add the contribution from BOTH friction and stochastic force to the
! coordinates, but ONLY the contribution from the friction forces to velocities
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
! include 'COMMON.NAMES'
real(kind=8),dimension(6*nres) :: stochforcvec,d_as_work1 !(MAXRES6) maxres6=6*maxres
real(kind=8) :: cos60 = 0.5d0, sin60 = 0.86602540378443864676d0
- integer :: i,j,ind,inres
+ integer :: i,j,ind,inres,mnum
! Revised 3/31/05 AL: correlation between random contributions to
! position and velocity increments included.
! The correlation coefficients are calculated at low-friction limit.
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres) &
! include 'COMMON.IOUNITS'
real(kind=8),dimension(3) :: aux,accel,accel_old
real(kind=8) :: dacc
- integer :: i,j
+ integer :: i,j,mnum
do j=1,3
! aux(j)=d_a(j,0)-d_a_old(j,0)
enddo
endif
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
! accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
accel_old(j)=accel_old(j)+d_a_old(j,i+nres)
enddo
endif
! Side chains
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
do j=1,3
epdriftij= &
dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
! include 'COMMON.IOUNITS'
! include 'COMMON.NAMES'
real(kind=8) :: T_half,fact
- integer :: i,j,inres
+ integer :: i,j,inres,mnum
!
T_half=2.0d0/(dimen3*Rb)*EK
fact=dsqrt(1.0d0+(d_time/tau_bath)*(t_bath/T_half-1.0d0))
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
d_t(j,inres)=fact*d_t(j,inres)
character(len=50) :: tytul
logical :: file_exist
!el common /gucio/ cm
- integer :: i,j,ipos,iq,iw,nft_sc,iretcode,nfun,itime,ierr
+ integer :: i,j,ipos,iq,iw,nft_sc,iretcode,nfun,itime,ierr,mnum
real(kind=8) :: etot,tt0
logical :: fail
! if the friction coefficients do not depend on surface area
if (lang.gt.0 .and. .not.surfarea) then
do i=nnt,nct-1
- stdforcp(i)=stdfp*dsqrt(gamp)
+ mnum=molnum(i)
+ stdforcp(i)=stdfp(mnum)*dsqrt(gamp(mnum))
enddo
do i=nnt,nct
- stdforcsc(i)=stdfsc(iabs(itype(i))) &
- *dsqrt(gamsc(iabs(itype(i))))
+ mnum=molnum(i)
+ stdforcsc(i)=stdfsc(iabs(itype(i,mnum)),mnum) &
+ *dsqrt(gamsc(iabs(itype(i,mnum)),mnum))
enddo
endif
! Open the pdb file for snapshotshots
endif
call random_vel
totT=0.0d0
+ totTafm=totT
endif
else
! Generate initial velocities
write(iout,*) "Initial velocities randomly generated"
call random_vel
totT=0.0d0
+ totTafm=totT
endif
! rest2name = prefix(:ilen(prefix))//'.rst'
if(me.eq.king.or..not.out1file)then
write (iout,*) "vcm right after adjustment:"
write (iout,*) (vcm(j),j=1,3)
endif
- if (.not.rest) then
+ if ((.not.rest).and.(indpdb.eq.0)) then
call chainbuild
if(iranconf.ne.0) then
if (overlapsc) then
real (kind=8),allocatable,dimension(:,:) :: matold
#endif
#endif
- integer :: i,j,ii,k,ind,mark,imark
+ integer :: i,j,ii,k,ind,mark,imark,mnum
! Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
! First generate velocities in the eigenspace of the G matrix
! write (iout,*) "Calling random_vel dimen dimen3",dimen,dimen3
Ek1=0.0d0
ii=0
do i=nnt,nct
- if (itype(i).eq.10) then
+! if (itype(i,1).eq.10) then
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
+ .or.(mnum.eq.5)) then
j=ii+3
else
j=ii+6
if (i.lt.nct) then
do k=1,3
! write (iout,*) "k",k," ii+k",ii+k," ii+j+k",ii+j+k,"EK1",Ek1
- Ek1=Ek1+0.5d0*mp*((d_t_work(ii+j+k)+d_t_work_new(ii+k))/2)**2+&
- 0.5d0*0.25d0*IP*(d_t_work(ii+j+k)-d_t_work_new(ii+k))**2
+ Ek1=Ek1+0.5d0*mp(mnum)*((d_t_work(ii+j+k)+d_t_work_new(ii+k))/2)**2+&
+ 0.5d0*0.25d0*IP(mnum)*(d_t_work(ii+j+k)-d_t_work_new(ii+k))**2
enddo
endif
- if (itype(i).ne.10) ii=ii+3
- write (iout,*) "i",i," itype",itype(i)," mass",msc(itype(i))
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) ii=ii+3
+ write (iout,*) "i",i," itype",itype(i,mnum)," mass",msc(itype(i,mnum),mnum)
write (iout,*) "ii",ii
do k=1,3
ii=ii+1
write (iout,*) "k",k," ii",ii,"EK1",EK1
- if (iabs(itype(i)).ne.10) Ek1=Ek1+0.5d0*Isc(iabs(itype(i)))*(d_t_work(ii)-d_t_work(ii-3))**2
- Ek1=Ek1+0.5d0*msc(iabs(itype(i)))*d_t_work(ii)**2
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))&
+ Ek1=Ek1+0.5d0*Isc(iabs(itype(i,mnum),mnum))*(d_t_work(ii)-d_t_work(ii-3))**2
+ Ek1=Ek1+0.5d0*msc(iabs(itype(i,mnum)),mnum)*d_t_work(ii)**2
enddo
write (iout,*) "i",i," ii",ii
enddo
d_t(k,j)=d_t_work(ind)
ind=ind+1
enddo
- if (itype(j).ne.10 .and. itype(j).ne.ntyp1) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))
do k=1,3
d_t(k,j+nres)=d_t_work(ind)
ind=ind+1
d_t(j,0)=d_t(j,nnt)
enddo
do i=nnt,nct
- if (itype(i).eq.10) then
+! if (itype(i,1).eq.10) then
+ mnum=molnum(i)
+ if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
+ .or.(mnum.eq.5))
do j=1,3
d_t(j,i)=d_t(j,i+1)-d_t(j,i)
enddo
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
ind=ind+1
d_t(j,i+nres)=d_t_work(ind)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
dc(j,inres)=dc_work(ind+j)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
do j=1,3
dc_work(ind+j)=dc_old(j,i+nres)
d_t_work(ind+j)=d_t_old(j,i+nres)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
inres=i+nres
do j=1,3
dc(j,inres)=dc_work(ind+j)
ind=ind+3
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))
+! if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
inres=i+nres
do j=1,3
d_t(j,inres)=d_t_work(ind+j)
real(kind=8),dimension(3,3) :: Im,Imcp,eigvec,Id
real(kind=8),dimension(3) :: pr,eigval,L,vp,vrot
- real(kind=8) :: M_SC,mag,mag2
+ real(kind=8) :: M_SC,mag,mag2,M_PEP
real(kind=8),dimension(3,0:nres) :: vpp !(3,0:MAXRES)
real(kind=8),dimension(3) :: vs_p,pp,incr,v
real(kind=8),dimension(3,3) :: pr1,pr2
!el common /gucio/ cm
- integer :: iti,inres,i,j,k
+ integer :: iti,inres,i,j,k,mnum
do i=1,3
do j=1,3
Im(i,j)=0.0d0
vrot(i)=0.0d0
enddo
! calculating the center of the mass of the protein
+ M_PEP=0.0d0
do i=nnt,nct-1
+ mnum=molnum(i)
+ if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
+ M_PEP=M_PEP+mp(mnum)
do j=1,3
- cm(j)=cm(j)+c(j,i)+0.5d0*dc(j,i)
+ cm(j)=cm(j)+(c(j,i)+0.5d0*dc(j,i))*mp(mnum)
enddo
enddo
- do j=1,3
- cm(j)=mp*cm(j)
- enddo
+! do j=1,3
+! cm(j)=mp(1)*cm(j)
+! enddo
M_SC=0.0d0
do i=nnt,nct
- iti=iabs(itype(i))
- M_SC=M_SC+msc(iabs(iti))
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
+ M_SC=M_SC+msc(iabs(iti),mnum)
inres=i+nres
do j=1,3
- cm(j)=cm(j)+msc(iabs(iti))*c(j,inres)
+ cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)
enddo
enddo
do j=1,3
- cm(j)=cm(j)/(M_SC+(nct-nnt)*mp)
+ cm(j)=cm(j)/(M_SC+M_PEP)
enddo
do i=nnt,nct-1
+ mnum=molnum(i)
do j=1,3
pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
enddo
- Im(1,1)=Im(1,1)+mp*(pr(2)*pr(2)+pr(3)*pr(3))
- Im(1,2)=Im(1,2)-mp*pr(1)*pr(2)
- Im(1,3)=Im(1,3)-mp*pr(1)*pr(3)
- Im(2,3)=Im(2,3)-mp*pr(2)*pr(3)
- Im(2,2)=Im(2,2)+mp*(pr(3)*pr(3)+pr(1)*pr(1))
- Im(3,3)=Im(3,3)+mp*(pr(1)*pr(1)+pr(2)*pr(2))
+ Im(1,1)=Im(1,1)+mp(mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
+ Im(1,2)=Im(1,2)-mp(mnum)*pr(1)*pr(2)
+ Im(1,3)=Im(1,3)-mp(mnum)*pr(1)*pr(3)
+ Im(2,3)=Im(2,3)-mp(mnum)*pr(2)*pr(3)
+ Im(2,2)=Im(2,2)+mp(mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
+ Im(3,3)=Im(3,3)+mp(mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
enddo
do i=nnt,nct
- iti=iabs(itype(i))
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
inres=i+nres
do j=1,3
pr(j)=c(j,inres)-cm(j)
enddo
- Im(1,1)=Im(1,1)+msc(iabs(iti))*(pr(2)*pr(2)+pr(3)*pr(3))
- Im(1,2)=Im(1,2)-msc(iabs(iti))*pr(1)*pr(2)
- Im(1,3)=Im(1,3)-msc(iabs(iti))*pr(1)*pr(3)
- Im(2,3)=Im(2,3)-msc(iabs(iti))*pr(2)*pr(3)
- Im(2,2)=Im(2,2)+msc(iabs(iti))*(pr(3)*pr(3)+pr(1)*pr(1))
- Im(3,3)=Im(3,3)+msc(iabs(iti))*(pr(1)*pr(1)+pr(2)*pr(2))
+ Im(1,1)=Im(1,1)+msc(iabs(iti),mnum)*(pr(2)*pr(2)+pr(3)*pr(3))
+ Im(1,2)=Im(1,2)-msc(iabs(iti),mnum)*pr(1)*pr(2)
+ Im(1,3)=Im(1,3)-msc(iabs(iti),mnum)*pr(1)*pr(3)
+ Im(2,3)=Im(2,3)-msc(iabs(iti),mnum)*pr(2)*pr(3)
+ Im(2,2)=Im(2,2)+msc(iabs(iti),mnum)*(pr(3)*pr(3)+pr(1)*pr(1))
+ Im(3,3)=Im(3,3)+msc(iabs(iti),mnum)*(pr(1)*pr(1)+pr(2)*pr(2))
enddo
do i=nnt,nct-1
- Im(1,1)=Im(1,1)+Ip*(1-dc_norm(1,i)*dc_norm(1,i))* &
+ mnum=molnum(i)
+ Im(1,1)=Im(1,1)+Ip(mnum)*(1-dc_norm(1,i)*dc_norm(1,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
- Im(1,2)=Im(1,2)+Ip*(-dc_norm(1,i)*dc_norm(2,i))* &
+ Im(1,2)=Im(1,2)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(2,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
- Im(1,3)=Im(1,3)+Ip*(-dc_norm(1,i)*dc_norm(3,i))* &
+ Im(1,3)=Im(1,3)+Ip(mnum)*(-dc_norm(1,i)*dc_norm(3,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
- Im(2,3)=Im(2,3)+Ip*(-dc_norm(2,i)*dc_norm(3,i))* &
+ Im(2,3)=Im(2,3)+Ip(mnum)*(-dc_norm(2,i)*dc_norm(3,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
- Im(2,2)=Im(2,2)+Ip*(1-dc_norm(2,i)*dc_norm(2,i))* &
+ Im(2,2)=Im(2,2)+Ip(mnum)*(1-dc_norm(2,i)*dc_norm(2,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
- Im(3,3)=Im(3,3)+Ip*(1-dc_norm(3,i)*dc_norm(3,i))* &
+ Im(3,3)=Im(3,3)+Ip(mnum)*(1-dc_norm(3,i)*dc_norm(3,i))* &
vbld(i+1)*vbld(i+1)*0.25d0
enddo
do i=nnt,nct
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
- iti=iabs(itype(i))
+ mnum=molnum(i)
+! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
+ iti=iabs(itype(i,mnum))
inres=i+nres
- Im(1,1)=Im(1,1)+Isc(iti)*(1-dc_norm(1,inres)* &
+ Im(1,1)=Im(1,1)+Isc(iti,mnum)*(1-dc_norm(1,inres)* &
dc_norm(1,inres))*vbld(inres)*vbld(inres)
- Im(1,2)=Im(1,2)-Isc(iti)*(dc_norm(1,inres)* &
+ Im(1,2)=Im(1,2)-Isc(iti,mnum)*(dc_norm(1,inres)* &
dc_norm(2,inres))*vbld(inres)*vbld(inres)
- Im(1,3)=Im(1,3)-Isc(iti)*(dc_norm(1,inres)* &
+ Im(1,3)=Im(1,3)-Isc(iti,mnum)*(dc_norm(1,inres)* &
dc_norm(3,inres))*vbld(inres)*vbld(inres)
- Im(2,3)=Im(2,3)-Isc(iti)*(dc_norm(2,inres)* &
+ Im(2,3)=Im(2,3)-Isc(iti,mnum)*(dc_norm(2,inres)* &
dc_norm(3,inres))*vbld(inres)*vbld(inres)
- Im(2,2)=Im(2,2)+Isc(iti)*(1-dc_norm(2,inres)* &
+ Im(2,2)=Im(2,2)+Isc(iti,mnum)*(1-dc_norm(2,inres)* &
dc_norm(2,inres))*vbld(inres)*vbld(inres)
- Im(3,3)=Im(3,3)+Isc(iti)*(1-dc_norm(3,inres)* &
+ Im(3,3)=Im(3,3)+Isc(iti,mnum)*(1-dc_norm(3,inres)* &
dc_norm(3,inres))*vbld(inres)*vbld(inres)
endif
enddo
enddo
enddo
do i=nnt,nct
- if(itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
+! if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
+! if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
inres=i+nres
call vecpr(vrot(1),dc(1,inres),vp)
do j=1,3
! include 'COMMON.NAMES'
real(kind=8),dimension(3) :: L,cm,pr,vp,vrot,incr,v,pp
- integer :: iti,inres,i,j
+ integer :: iti,inres,i,j,mnum
! Calculate the angular momentum
do j=1,3
L(j)=0.0d0
incr(j)=d_t(j,0)
enddo
do i=nnt,nct-1
+ mnum=molnum(i)
do j=1,3
pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
enddo
enddo
call vecpr(pr(1),v(1),vp)
do j=1,3
- L(j)=L(j)+mp*vp(j)
+ L(j)=L(j)+mp(mnum)*vp(j)
enddo
do j=1,3
pr(j)=0.5d0*dc(j,i)
enddo
call vecpr(pr(1),pp(1),vp)
do j=1,3
- L(j)=L(j)+Ip*vp(j)
+ L(j)=L(j)+Ip(mnum)*vp(j)
enddo
enddo
do j=1,3
incr(j)=d_t(j,0)
enddo
do i=nnt,nct
- iti=iabs(itype(i))
+ mnum=molnum(i)
+ iti=iabs(itype(i,mnum))
inres=i+nres
do j=1,3
pr(j)=c(j,inres)-cm(j)
enddo
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
v(j)=incr(j)+d_t(j,inres)
enddo
! write (iout,*) "i",i," iti",iti," pr",(pr(j),j=1,3),
! & " v",(v(j),j=1,3)," vp",(vp(j),j=1,3)
do j=1,3
- L(j)=L(j)+msc(iabs(iti))*vp(j)
+ L(j)=L(j)+msc(iabs(iti),mnum)*vp(j)
enddo
! write (iout,*) "L",(l(j),j=1,3)
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
v(j)=incr(j)+d_t(j,inres)
enddo
call vecpr(dc(1,inres),d_t(1,inres),vp)
do j=1,3
- L(j)=L(j)+Isc(iti)*vp(j)
+ L(j)=L(j)+Isc(iti,mnum)*vp(j)
enddo
endif
do j=1,3
! include 'COMMON.IOUNITS'
real(kind=8),dimension(3) :: vcm,vv
real(kind=8) :: summas,amas
- integer :: i,j
+ integer :: i,j,mnum
do j=1,3
vcm(j)=0.0d0
enddo
summas=0.0d0
do i=nnt,nct
+ mnum=molnum(i)
if (i.lt.nct) then
- summas=summas+mp
+ summas=summas+mp(mnum)
do j=1,3
- vcm(j)=vcm(j)+mp*(vv(j)+0.5d0*d_t(j,i))
+ vcm(j)=vcm(j)+mp(mnum)*(vv(j)+0.5d0*d_t(j,i))
enddo
endif
- amas=msc(iabs(itype(i)))
+ amas=msc(iabs(itype(i,mnum)),mnum)
summas=summas+amas
- if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
+ if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
do j=1,3
vcm(j)=vcm(j)+amas*(vv(j)+d_t(j,i+nres))
enddo
if (lprn) write (iout,*) "RATTLE1"
nbond=nct-nnt
do i=nnt,nct
- if (itype(i).ne.10) nbond=nbond+1
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) nbond=nbond+1
enddo
! Make a folded form of the Ginv-matrix
ind=0
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ mnum=molnum(k)
+ if (itype(k,1).ne.10 .and. itype(k,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
jj=jj+1
do l=1,3
ind1=ind1+1
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))
ii=ii+1
do j=1,3
ind=ind+1
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
jj=jj+1
do l=1,3
ind1=ind1+1
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind1=ind1+1
do j=1,3
dC_uncor(j,ind1)=dC(j,i+nres)
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
ind=ind+1
do j=1,3
gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
x(ind)=vbld(i+1)**2-vbl**2
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
- x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i))**2
+ x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
endif
enddo
if (lprn) then
i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
+
ind=ind+1
write (iout,'(2i5,3f10.5,5x,e15.5)') &
i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
do j=1,3
xx=0.0d0
i,(dC(j,i),j=1,3),x(ind),xx
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))
ind=ind+1
- xx=vbld(i+nres)**2-vbldsc0(1,itype(i))**2
+ xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
i,(dC(j,i+nres),j=1,3),x(ind),xx
endif
i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
write (iout,'(2i5,3f10.5,5x,e15.5)') &
i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
ind=ind+1
do j=1,3
gdc(j,i,ind)=GGinv(i,ind)*dC(j,k+nres)
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
ind=ind+1
do j=1,nbond
Cmat(ind,j)=0.0d0
x(ind)=scalar(d_t(1,i),dC(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
ind=ind+1
x(ind)=scalar(d_t(1,i+nres),dC(1,i+nres))
endif
i,ind,(d_t(j,i),j=1,3),x(ind)
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
ind=ind+1
write (iout,'(2i5,3f10.5,5x,e15.5)') &
i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind)
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5)) then
ind=ind+1
do j=1,3
xx=0.0d0
i,ind,(d_t(j,i),j=1,3),x(ind),scalar(d_t(1,i),dC(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ mnum=molnum(i)
+ if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
+ .and.(mnum.ne.5))
ind=ind+1
write (iout,'(2i5,3f10.5,5x,2e15.5)') &
i+nres,ind,(d_t(j,i+nres),j=1,3),x(ind),&
!el common /przechowalnia/ GGinv,gdc,Cmat,nbond
!el common /przechowalnia/ nbond
integer :: max_rattle = 5
- logical :: lprn = .true., lprn1 = .true., not_done
+ logical :: lprn = .false., lprn1 = .false., not_done
real(kind=8) :: tol_rattle = 1.0d-5
integer :: nres2
nres2=2*nres
if (lprn) write (iout,*) "RATTLE_BROWN"
nbond=nct-nnt
do i=nnt,nct
- if (itype(i).ne.10) nbond=nbond+1
+ if (itype(i,1).ne.10) nbond=nbond+1
enddo
! Make a folded form of the Ginv-matrix
ind=0
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
jj=jj+1
do l=1,3
ind1=ind1+1
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ii=ii+1
do j=1,3
ind=ind+1
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
jj=jj+1
do l=1,3
ind1=ind1+1
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind1=ind1+1
do j=1,3
dC_uncor(j,ind1)=dC(j,i+nres)
enddo
enddo
do k=nnt,nct
- if (itype(k).ne.10) then
+ if (itype(k,1).ne.10) then
ind=ind+1
do j=1,3
gdc(j,i,ind)=GGinv(i,ind)*dC_old(j,k+nres)
x(ind)=vbld(i+1)**2-vbl**2
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
- x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i))**2
+ x(ind)=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
endif
enddo
if (lprn) then
i,ind,(d_t(j,i),j=1,3),scalar(d_t(1,i),dC_old(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
write (iout,'(2i5,3f10.5,5x,e15.5)') &
i+nres,ind,(d_t(j,i+nres),j=1,3),&
enddo
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
do j=1,3
xx=0.0d0
i,(dC(j,i),j=1,3),x(ind),xx
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
- xx=vbld(i+nres)**2-vbldsc0(1,itype(i))**2
+ xx=vbld(i+nres)**2-vbldsc0(1,itype(i,1))**2
write (iout,'(i5,3f10.5,5x,f10.5,e15.5)') &
i,(dC(j,i+nres),j=1,3),x(ind),xx
endif
i,ind,(d_t_new(j,i),j=1,3),scalar(d_t_new(1,i),dC_old(1,i))
enddo
do i=nnt,nct
- if (itype(i).ne.10) then
+ if (itype(i,1).ne.10) then
ind=ind+1
write (iout,'(2i5,3f10.5,5x,e15.5)') &
i+nres,ind,(d_t_new(j,i+nres),j=1,3),&
!el common /przechowalnia/ ginvfric
logical :: lprn = .false., checkmode = .false.
- integer :: i,j,ind,k,nres2,nres6
+ integer :: i,j,ind,k,nres2,nres6,mnum
nres2=2*nres
nres6=6*nres
ind=ind+3
enddo
do i=nnt,nct
- if ((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
+ mnum=molnum(i)
+ if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
+ .and.(mnum.ne.5)) then
do j=1,3
d_t_work(ind+j)=d_t(j,i+nres)
enddo
ind=ind+3
enddo
do i=nnt,nct
- if ((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
+ mnum=molnum(i)
+ if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
+ .and.(mnum.ne.5)) then
+! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
do j=1,3
friction(j,i+nres)=fric_work(ind+j)
enddo
real(kind=8) :: work(8*2*nres)
integer :: iwork(2*nres)
!el common /przechowalnia/ ginvfric,Ghalf,fcopy
- integer :: ii,iti,k,l,nzero,nres2,nres6,ierr
+ integer :: ii,iti,k,l,nzero,nres2,nres6,ierr,mnum
#ifdef MPI
if (fg_rank.ne.king) goto 10
#endif
! Load the friction coefficients corresponding to peptide groups
ind1=0
do i=nnt,nct-1
+ mnum=molnum(i)
ind1=ind1+1
- gamvec(ind1)=gamp
+ gamvec(ind1)=gamp(mnum)
enddo
! Load the friction coefficients corresponding to side chains
m=nct-nnt
ind=0
- gamsc(ntyp1)=1.0d0
+ do j=1,2
+ gamsc(ntyp1_molec(j),j)=1.0d0
+ enddo
do i=nnt,nct
+ mnum=molnum(i)
ind=ind+1
ii = ind+m
- iti=itype(i)
- gamvec(ii)=gamsc(iabs(iti))
+ iti=itype(i,mnum)
+ gamvec(ii)=gamsc(iabs(iti),mnum)
enddo
if (surfarea) call sdarea(gamvec)
! if (lprn) then
real(kind=8) :: highb2,sig2,forcvec(6*nres),stochforcvec(6*nres)
real(kind=8) :: time00
logical :: lprn = .false.
- integer :: i,j,ind
+ integer :: i,j,ind,mnum
do i=0,2*nres
do j=1,3
do j=1,3
ff(j)=ff(j)+force(j,i)
enddo
- if (itype(i+1).ne.ntyp1) then
+! if (itype(i+1,1).ne.ntyp1) then
+ mnum=molnum(i)
+ if (itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
do j=1,3
stochforc(j,i)=stochforc(j,i)+force(j,i+nres+1)
ff(j)=ff(j)+force(j,i+nres+1)
stochforc(j,0)=ff(j)+force(j,nnt+nres)
enddo
do i=nnt,nct
- if ((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
+ mnum=molnum(i)
+ if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
+ .and.(mnum.ne.5)) then
+! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
do j=1,3
stochforc(j,i+nres)=force(j,i+nres)
enddo
ind=ind+3
enddo
do i=nnt,nct
- if ((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
+ mnum=molnum(i)
+ if ((itype(i,1).ne.10).and.(itype(i,mnum).ne.ntyp1_molec(mnum))&
+ .and.(mnum.ne.5)) then
+! if ((itype(i,1).ne.10).and.(itype(i,1).ne.ntyp1)) then
do j=1,3
stochforcvec(ind+j)=stochforc(j,i+nres)
enddo
real(kind=8),parameter :: twosix = 1.122462048309372981d0
logical :: lprn = .false.
real(kind=8) :: probe,area,ratio
- integer :: i,j,ind,iti
+ integer :: i,j,ind,iti,mnum
!
! determine new friction coefficients every few SD steps
!
enddo
! Load peptide group radii
do i=nnt,nct-1
- radius(i)=pstok
+ mnum=molnum(i)
+ radius(i)=pstok(mnum)
enddo
! Load side chain radii
do i=nnt,nct
- iti=itype(i)
- radius(i+nres)=restok(iti)
+ mnum=molnum(i)
+ iti=itype(i,mnum)
+ radius(i+nres)=restok(iti,mnum)
enddo
! do i=1,2*nres
! write (iout,*) "i",i," radius",radius(i)
ind=ind+1
gamvec(ind) = ratio * gamvec(ind)
enddo
- stdforcp(i)=stdfp*dsqrt(gamvec(ind))
+ mnum=molnum(i)
+ stdforcp(i)=stdfp(mnum)*dsqrt(gamvec(ind))
if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcp(i)
endif
enddo
ind=ind+1
gamvec(ind) = ratio * gamvec(ind)
enddo
- stdforcsc(i)=stdfsc(itype(i))*dsqrt(gamvec(ind))
+ mnum=molnum(i)
+ stdforcsc(i)=stdfsc(itype(i,mnum),mnum)*dsqrt(gamvec(ind))
if (lprn) write (iout,'(2f10.5)') gamvec(ind),stdforcsc(i)
endif
enddo
projects / unres4.git / blobdiff