added preminim

diff --git a/source/unres/MD.f90 b/source/unres/MD.f90
index 7aaac15..e34b384 100644 (file)
--- a/source/unres/MD.f90
+++ b/source/unres/MD.f90
@@ -2507,9 +2507,9 @@
        write (iout,*) "vcm right after adjustment:"
        write (iout,*) (vcm(j),j=1,3) 
       endif
        write (iout,*) "vcm right after adjustment:"
        write (iout,*) (vcm(j),j=1,3) 
       endif

-      if ((.not.rest).and.(indpdb.eq.0)) then          
-         call chainbuild
-         if(iranconf.ne.0) then
+      if (.not.rest) then              
+!         call chainbuild
+         if(iranconf.ne.0 .or.indpdb.gt.0.and..not.unres_pdb .or.preminim) then

           if (overlapsc) then 
            print *, 'Calling OVERLAP_SC'
            call overlap_sc(fail)
           if (overlapsc) then 
            print *, 'Calling OVERLAP_SC'
            call overlap_sc(fail)

diff --git a/source/unres/data/MD_data.f90 b/source/unres/data/MD_data.f90
index d0fa7e6..3273cfc 100644 (file)
--- a/source/unres/data/MD_data.f90
+++ b/source/unres/data/MD_data.f90
@@ -104,4 +104,5 @@
 !      COMMON /BANII/ D
       real(kind=8),DIMENSION(:),allocatable :: D_ban !(MAXRES6) maxres6=6*maxres
 !-----------------------------------------------------------------------------
 !      COMMON /BANII/ D
       real(kind=8),DIMENSION(:),allocatable :: D_ban !(MAXRES6) maxres6=6*maxres
 !-----------------------------------------------------------------------------

+      logical preminim ! pre-minimizaation flag

       end module MD_data
       end module MD_data

diff --git a/source/unres/data/geometry_data.f90 b/source/unres/data/geometry_data.f90
index 49357af..eb64d82 100644 (file)
--- a/source/unres/data/geometry_data.f90
+++ b/source/unres/data/geometry_data.f90
@@ -43,7 +43,7 @@
       integer,parameter :: maxlob=5
 !-----------------------------------------------------------------------------
 ! Max number of symetric chains
       integer,parameter :: maxlob=5
 !-----------------------------------------------------------------------------
 ! Max number of symetric chains

-      integer,parameter :: maxsym=50
+      integer,parameter :: maxsym=80!50

       integer,parameter :: maxperm=120
 !-----------------------------------------------------------------------------
 ! common.var
       integer,parameter :: maxperm=120
 !-----------------------------------------------------------------------------
 ! common.var

diff --git a/source/unres/io_config.f90 b/source/unres/io_config.f90
index ee1402f..b52f157 100644 (file)
--- a/source/unres/io_config.f90
+++ b/source/unres/io_config.f90
@@ -2899,7 +2899,7 @@
       if(.not. allocated(istype)) allocate(istype(maxres))
       do i=1,100000
         read (ipdbin,'(a80)',end=10) card
       if(.not. allocated(istype)) allocate(istype(maxres))
       do i=1,100000
         read (ipdbin,'(a80)',end=10) card

-!       write (iout,'(a)') card
+       write (iout,'(a)') card

         if (card(:5).eq.'HELIX') then
           nhfrag=nhfrag+1
           lsecondary=.true.
         if (card(:5).eq.'HELIX') then
           nhfrag=nhfrag+1
           lsecondary=.true.

@@ -3362,10 +3362,10 @@
       if (lprn) then
       write (iout,'(/a)') &
         "Cartesian coordinates of the reference structure"
       if (lprn) then
       write (iout,'(/a)') &
         "Cartesian coordinates of the reference structure"

-      write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+      write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &

        "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
       do ires=1,nres
        "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
       do ires=1,nres

-        write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') &
+        write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &

           (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
           (c(j,ires+nres),j=1,3)
       enddo
           (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
           (c(j,ires+nres),j=1,3)
       enddo

@@ -3376,7 +3376,7 @@
        write (iout,'(a)') &
          "Backbone and SC coordinates as read from the PDB"
        do ires=1,nres
        write (iout,'(a)') &
          "Backbone and SC coordinates as read from the PDB"
        do ires=1,nres

-        write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)') &
+        write (iout,'(i5,i3,2x,a,3f8.3,5x,3f8.3)') &

           ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
           (c(j,nres+ires),j=1,3)
        enddo
           ires,itype(ires,1),restyp(itype(ires,1),1),(c(j,ires),j=1,3),&
           (c(j,nres+ires),j=1,3)
        enddo

@@ -3443,10 +3443,10 @@
       if (lprn) then
       write (iout,'(/a)') &
         "Cartesian coordinates of the reference structure after sorting"
       if (lprn) then
       write (iout,'(/a)') &
         "Cartesian coordinates of the reference structure after sorting"

-      write (iout,'(a,3(3x,a5),5x,3(3x,a5))') &
+      write (iout,'(a,16x,3(3x,a5),5x,3(3x,a5))') &

        "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
       do ires=1,nres
        "Residue","X(CA)","Y(CA)","Z(CA)","X(SC)","Y(SC)","Z(SC)"
       do ires=1,nres

-        write (iout,'(5(a3,1x),i3,3f8.3,5x,3f8.3)') &
+        write (iout,'(5(a3,1x),i5,3f8.3,5x,3f8.3)') &

           (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
           (c(j,ires+nres),j=1,3)
       enddo
           (restyp(itype(ires,j),j),j=1,5),ires,(c(j,ires),j=1,3),&
           (c(j,ires+nres),j=1,3)
       enddo

@@ -3534,7 +3534,7 @@
         write (iout,*) "symetr", symetr
       do i=1,nres
       lll=lll+1
         write (iout,*) "symetr", symetr
       do i=1,nres
       lll=lll+1

-!c      write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
+!      write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)

       if (i.gt.1) then
       if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
       chain_length=lll-1
       if (i.gt.1) then
       if ((itype(i-1,1).eq.ntyp1).and.(i.gt.2)) then
       chain_length=lll-1

@@ -3563,7 +3563,7 @@
 !       write (iout,*) "spraw lancuchy",chain_length,symetr
 !       do i=1,4
 !         do kkk=1,chain_length
 !       write (iout,*) "spraw lancuchy",chain_length,symetr
 !       do i=1,4
 !         do kkk=1,chain_length

-!           write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
+!           write (iout,*) itype(kkk,1),(chain_rep(j,kkk,i), j=1,3)

 !         enddo
 !        enddo
 ! enddiagnostic
 !         enddo
 !        enddo
 ! enddiagnostic

@@ -3586,7 +3586,7 @@
         cou=0
         do kkk=1,symetr
          icha=tabperm(i,kkk)
         cou=0
         do kkk=1,symetr
          icha=tabperm(i,kkk)

-!         write (iout,*) i,icha
+         write (iout,*) i,icha

          do lll=1,chain_length
           cou=cou+1
            if (cou.le.nres) then
          do lll=1,chain_length
           cou=cou+1
            if (cou.le.nres) then

@@ -3594,7 +3594,7 @@
             kupa=mod(lll,chain_length)
             iprzes=(kkk-1)*chain_length+lll
             if (kupa.eq.0) kupa=chain_length
             kupa=mod(lll,chain_length)
             iprzes=(kkk-1)*chain_length+lll
             if (kupa.eq.0) kupa=chain_length

-!            write (iout,*) "kupa", kupa
+            write (iout,*) "kupa", kupa

             cref(j,iprzes,i)=chain_rep(j,kupa,icha)
             cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
           enddo
             cref(j,iprzes,i)=chain_rep(j,kupa,icha)
             cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
           enddo

@@ -3613,11 +3613,11 @@
       cref(3,i,kkk),cref(1,nres+i,kkk),&
       cref(2,nres+i,kkk),cref(3,nres+i,kkk)
       enddo
       cref(3,i,kkk),cref(1,nres+i,kkk),&
       cref(2,nres+i,kkk),cref(3,nres+i,kkk)
       enddo

-  100 format (//'              alpha-carbon coordinates       ',&
+  100 format (//'                alpha-carbon coordinates       ',&

                 '     centroid coordinates'/ &
                 '       ', 6X,'X',11X,'Y',11X,'Z', &
                                 10X,'X',11X,'Y',11X,'Z')
                 '     centroid coordinates'/ &
                 '       ', 6X,'X',11X,'Y',11X,'Z', &
                                 10X,'X',11X,'Y',11X,'Z')

-  110 format (a,'(',i3,')',6f12.5)
+  110 format (a,'(',i5,')',6f12.5)

      
       enddo
 !c enddiag
      
       enddo
 !c enddiag

@@ -4066,6 +4066,10 @@
       large = index(controlcard,"LARGE").gt.0
       print_compon = index(controlcard,"PRINT_COMPON").gt.0
       rattle = index(controlcard,"RATTLE").gt.0
       large = index(controlcard,"LARGE").gt.0
       print_compon = index(controlcard,"PRINT_COMPON").gt.0
       rattle = index(controlcard,"RATTLE").gt.0

+      preminim=(index(controlcard,'PREMINIM').gt.0)
+      write (iout,*) "PREMINIM ",preminim
+      dccart=(index(controlcard,'CART').gt.0)
+      if (preminim) call read_minim

 !  if performing umbrella sampling, fragments constrained are read from the fragment file 
       nset=0
       if(usampl) then
 !  if performing umbrella sampling, fragments constrained are read from the fragment file 
       nset=0
       if(usampl) then