include 'COMMON.IOUNITS'
include 'COMMON.NAMES'
include 'COMMON.INTERACT'
- logical lprn
+ double precision e1(3),e2(3),e3(3)
+ logical lprn,perbox,fail
C Set lprn=.true. for debugging
lprn = .false.
+ perbox=.false.
+ fail=.false.
+ print *, 'enter chainbuild'
+ if (perbox) then
+ cost=dcos(theta(3))
+ sint=dsin(theta(3))
+ print *,'before refsys'
+ call refsys(2,3,4,e1,e2,e3,fail)
+ print *,'after refsys'
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ dc(1,0)=c(1,1)
+ dc(2,0)=c(2,1)
+ dc(3,0)=c(3,1)
+ print *,'dc',dc(1,0),dc(2,0),dc(3,0)
+ dc(1,1)=c(1,2)-c(1,1)
+ dc(2,1)=c(2,2)-c(2,1)
+ dc(3,1)=c(3,2)-c(3,1)
+ dc(1,2)=c(1,3)-c(1,2)
+ dc(2,2)=c(2,3)-c(2,2)
+ dc(3,2)=c(3,3)-c(3,2)
+ t(1,1,1)=e1(1)
+ t(1,2,1)=e1(2)
+ t(1,3,1)=e1(3)
+ t(2,1,1)=e2(1)
+ t(2,2,1)=e2(2)
+ t(2,3,1)=e2(3)
+ t(3,1,1)=e3(1)
+ t(3,2,1)=e3(2)
+ t(3,3,1)=e3(3)
+ veclen=0.0d0
+ do i=1,3
+ veclen=veclen+(c(i,2)-c(i,1))**2
+ enddo
+ veclen=sqrt(veclen)
+ r(1,1,1)= 1.0D0
+ r(1,2,1)= 0.0D0
+ r(1,3,1)= 0.0D0
+ r(2,1,1)= 0.0D0
+ r(2,2,1)= 1.0D0
+ r(2,3,1)= 0.0D0
+ r(3,1,1)= 0.0D0
+ r(3,2,1)= 0.0D0
+ r(3,3,1)= 1.0D0
+ do i=1,3
+ do j=1,3
+ rt(i,j,1)=t(i,j,1)
+ enddo
+ enddo
+ do i=1,3
+ do j=1,3
+ prod(i,j,1)=0.0D0
+ prod(i,j,2)=t(i,j,1)
+ enddo
+ prod(i,i,1)=1.0D0
+ enddo
+ call locate_side_chain(2)
+ do i=4,nres
+#ifdef OSF
+ theti=theta(i)
+ if (theti.ne.theti) theti=100.0
+ phii=phi(i)
+ if (phii.ne.phii) phii=180.0
+#else
+ theti=theta(i)
+ phii=phi(i)
+#endif
+ cost=dcos(theti)
+ sint=dsin(theti)
+ cosphi=dcos(phii)
+ sinphi=dsin(phii)
+* Define the matrices of the rotation about the virtual-bond valence angles
+* theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
+* program), R(i,j,k), and, the cumulative matrices of rotation RT
+ t(1,1,i-2)=-cost
+ t(1,2,i-2)=-sint
+ t(1,3,i-2)= 0.0D0
+ t(2,1,i-2)=-sint
+ t(2,2,i-2)= cost
+ t(2,3,i-2)= 0.0D0
+ t(3,1,i-2)= 0.0D0
+ t(3,2,i-2)= 0.0D0
+ t(3,3,i-2)= 1.0D0
+ r(1,1,i-2)= 1.0D0
+ r(1,2,i-2)= 0.0D0
+ r(1,3,i-2)= 0.0D0
+ r(2,1,i-2)= 0.0D0
+ r(2,2,i-2)=-cosphi
+ r(2,3,i-2)= sinphi
+ r(3,1,i-2)= 0.0D0
+ r(3,2,i-2)= sinphi
+ r(3,3,i-2)= cosphi
+ rt(1,1,i-2)=-cost
+ rt(1,2,i-2)=-sint
+ rt(1,3,i-2)=0.0D0
+ rt(2,1,i-2)=sint*cosphi
+ rt(2,2,i-2)=-cost*cosphi
+ rt(2,3,i-2)=sinphi
+ rt(3,1,i-2)=-sint*sinphi
+ rt(3,2,i-2)=cost*sinphi
+ rt(3,3,i-2)=cosphi
+ call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
+ do j=1,3
+ dc_norm(j,i-1)=prod(j,1,i-1)
+ dc(j,i-1)=vbld(i)*prod(j,1,i-1)
+ enddo
+ call locate_side_chain(i-1)
+ enddo
+ else
C
C Define the origin and orientation of the coordinate system and locate the
C first three CA's and SC(2).
1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
endif
-
+ endif
return
end
c-------------------------------------------------------------------------
dc_norm(3,1)=0.0D0
do j=1,3
dc_norm(j,2)=prod(j,1,2)
- dc(j,2)=vbld(3)*prod(j,1,2)
- c(j,3)=c(j,2)+dc(j,2)
+ dc(j,2)=vbld(3)*prod(j,1,2)
+ c(j,3)=c(j,2)+dc(j,2)
enddo
call locate_side_chain(2)
return
enddo
return
end
+c------------------------------------------
+ subroutine returnbox
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.CONTROL'
+ include 'COMMON.VAR'
+ include 'COMMON.MD'
+#ifndef LANG0
+ include 'COMMON.LANGEVIN'
+#else
+ include 'COMMON.LANGEVIN.lang0'
+#endif
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.GEO'
+ include 'COMMON.LOCAL'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.NAMES'
+ include 'COMMON.TIME1'
+ include 'COMMON.REMD'
+ include 'COMMON.SETUP'
+ include 'COMMON.MUCA'
+ include 'COMMON.HAIRPIN'
+C change suggested by Ana - begin
+ integer allareout
+C change suggested by Ana - end
+ j=1
+ chain_beg=1
+C do i=1,nres
+C write(*,*) 'initial', i,j,c(j,i)
+C enddo
+C change suggested by Ana - begin
+ allareout=1
+C change suggested by Ana -end
+ do i=1,nres-1
+ if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then
+ chain_end=i
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxxsize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,chain_end
+ c(j,k)=c(j,k)-ireturnval*boxxsize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
+ enddo
+C Suggested by Ana
+ if (chain_beg.eq.1)
+ & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
+C Suggested by Ana -end
+ endif
+ chain_beg=i+1
+ allareout=1
+ else
+ if (int(c(j,i)/boxxsize).eq.0) allareout=0
+ endif
+ enddo
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxxsize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,nres
+ c(j,k)=c(j,k)-ireturnval*boxxsize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
+ enddo
+ endif
+C NO JUMP
+C do i=1,nres
+C write(*,*) 'befor no jump', i,j,c(j,i)
+C enddo
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+C print *,'diff', difference
+ if (difference.gt.boxxsize/2.0) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxxsize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
+ enddo
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+ if (difference.gt.boxxsize/2.0) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxxsize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
+ enddo
+
+C do i=1,nres
+C write(*,*) 'after no jump', i,j,c(j,i)
+C enddo
+
+C NOW Y dimension
+C suggesed by Ana begins
+ allareout=1
+C suggested by Ana ends
+ j=2
+ chain_beg=1
+ do i=1,nres-1
+ if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then
+ chain_end=i
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxysize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,chain_end
+ c(j,k)=c(j,k)-ireturnval*boxysize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
+ enddo
+C Suggested by Ana
+ if (chain_beg.eq.1)
+ & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
+C Suggested by Ana -end
+ endif
+ chain_beg=i+1
+ allareout=1
+ else
+ if (int(c(j,i)/boxysize).eq.0) allareout=0
+ endif
+ enddo
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxysize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,nres
+ c(j,k)=c(j,k)-ireturnval*boxysize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
+ enddo
+ endif
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+ if (difference.gt.boxysize/2.0) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxysize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
+ enddo
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+ if (difference.gt.boxysize/2.0) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxysize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
+ enddo
+C Now Z dimension
+C Suggested by Ana -begins
+ allareout=1
+C Suggested by Ana -ends
+ j=3
+ chain_beg=1
+ do i=1,nres-1
+ if ((itype(i).eq.ntyp1).and.(itype(i+1).eq.ntyp1)) then
+ chain_end=i
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxysize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,chain_end
+ c(j,k)=c(j,k)-ireturnval*boxzsize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
+ enddo
+C Suggested by Ana
+ if (chain_beg.eq.1)
+ & dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
+C Suggested by Ana -end
+ endif
+ chain_beg=i+1
+ allareout=1
+ else
+ if (int(c(j,i)/boxzsize).eq.0) allareout=0
+ endif
+ enddo
+ if (allareout.eq.1) then
+ ireturnval=int(c(j,i)/boxzsize)
+ if (c(j,i).le.0) ireturnval=ireturnval-1
+ do k=chain_beg,nres
+ c(j,k)=c(j,k)-ireturnval*boxzsize
+ c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
+ enddo
+ endif
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+ if (difference.gt.(boxzsize/2.0)) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxzsize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
+ enddo
+ nojumpval=0
+ do i=2,nres
+ if (itype(i).eq.ntyp1 .and. itype(i-1).eq.ntyp1) then
+ difference=abs(c(j,i-1)-c(j,i))
+ if (difference.gt.boxzsize/2.0) then
+ if (c(j,i-1).gt.c(j,i)) then
+ nojumpval=1
+ else
+ nojumpval=-1
+ endif
+ else
+ nojumpval=0
+ endif
+ endif
+ c(j,i)=c(j,i)+nojumpval*boxzsize
+ c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
+ enddo
+
+ return
+ end
+
projects / unres.git / blobdiff