From: Adam Liwo <adam@matrix.chem.cornell.edu>
Date: Sun, 13 May 2012 06:16:52 +0000 (-0400)
Subject: 5/13/2012 by Adam
X-Git-Tag: v.3.2~80^2~11^2~12
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=f754eecac3c8a4547d905cca354f9a0db1531729

5/13/2012 by Adam

1. Added options to run simulations with NMR-type distance restraints;
introduced array dhpb1 to store right borders of distance restraints
(left borders stored in dhpb, if dhpb1(i).eq.0 ith restraint is harmonic type,
> 0, quartic (NMR-like) type).

2. Added option to imposed either Calpha or SC (Cbeta) restraints; the pertinent
array is ibecacarb.

3. The above changes have been introduced in readrtns.F and energy_p_new_barrier.F
Cleaned excessive output in MREMD.F (energies at exchange)

4. prng.f replaces prng_32.F in Intel Makefiles; program hangs up with prng_32
---

diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
index ba5a1a7..b5077e8 100755
Binary files a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe and b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe differ
diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
index f772e87..39b0d89 100755
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ
diff --git a/source/unres/src_MD/COMMON.SBRIDGE b/source/unres/src_MD/COMMON.SBRIDGE
index 4cc80c8..d75482c 100644
--- a/source/unres/src_MD/COMMON.SBRIDGE
+++ b/source/unres/src_MD/COMMON.SBRIDGE
@@ -2,10 +2,10 @@
       integer ns,nss,nfree,iss
       common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,
      & ns,nss,nfree,iss(maxss)
-      double precision dhpb,forcon
+      double precision dhpb,dhpb1,forcon
       integer ihpb,jhpb,nhpb
-      common /links/ dhpb(maxdim),forcon(maxdim),ihpb(maxdim),
-     & jhpb(maxdim),nhpb
+      common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
+     & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
       double precision weidis
       common /restraints/ weidis
       integer link_start,link_end
diff --git a/source/unres/src_MD/MD_A-MTS.F b/source/unres/src_MD/MD_A-MTS.F
index 29e4fcb..acbffa9 100644
--- a/source/unres/src_MD/MD_A-MTS.F
+++ b/source/unres/src_MD/MD_A-MTS.F
@@ -1806,6 +1806,7 @@ c      rest2name = prefix(:ilen(prefix))//'.rst'
          write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
      &   (d_t(j,i+nres),j=1,3)
        enddo 		 	 
+       call flush(iout)
 c  Zeroing the total angular momentum of the system
        write(iout,*) "Calling the zero-angular 
      & momentum subroutine"
@@ -1823,6 +1824,7 @@ c Removing the velocity of the center of mass
       if(me.eq.king.or..not.out1file)then
        write (iout,*) "vcm right after adjustment:"
        write (iout,*) (vcm(j),j=1,3) 
+       call flush(iout)
       endif
       if (.not.rest) then	  	
          call chainbuild
@@ -2078,6 +2080,7 @@ c          write (iout,*) "i",i," ii",ii," geigen",geigen(i),
 c     &      " d_t_work_new",d_t_work_new(ii)
         enddo
       enddo
+      call flush(iout)
 c diagnostics
 c      Ek1=0.0d0
 c      ii=0
@@ -2116,6 +2119,7 @@ c Transfer to the d_t vector
 c      do i=0,nres-1
 c        write (iout,*) "d_t",i,(d_t(j,i),j=1,3)
 c      enddo
+c      call flush(iout)
       do i=nnt,nct
         if (itype(i).ne.10) then
           do j=1,3
diff --git a/source/unres/src_MD/MD_A-MTS.o b/source/unres/src_MD/MD_A-MTS.o
new file mode 100644
index 0000000..540b734
Binary files /dev/null and b/source/unres/src_MD/MD_A-MTS.o differ
diff --git a/source/unres/src_MD/MP.o b/source/unres/src_MD/MP.o
new file mode 100644
index 0000000..866b109
Binary files /dev/null and b/source/unres/src_MD/MP.o differ
diff --git a/source/unres/src_MD/MREMD.F b/source/unres/src_MD/MREMD.F
index 9ddb9e9..576e43d 100644
--- a/source/unres/src_MD/MREMD.F
+++ b/source/unres/src_MD/MREMD.F
@@ -782,6 +782,7 @@ ctime            call flush(iout)
                remd_t_bath(i)=remd_ene(n_ene+1,i)
                iremd_iset(i)=remd_ene(n_ene+2,i)
             enddo
+#ifdef DEBUG
             if(lmuca) then
 co             write(iout,*) 'REMD exchange temp,ene,elow,ehigh'
              do i=1,nodes
@@ -795,20 +796,27 @@ co             write(iout,*) 'REMD exchange temp,ene,elow,ehigh'
                 write(iout,'(6f12.5)') (remd_ene(j,i),j=1,n_ene)
               enddo
             endif
+#endif
 c-------------------------------------           
            IF(.not.usampl.and.hremd.eq.0) THEN
+#ifdef DEBUG
             write (iout,*) "Enter exchnge, remd_m",remd_m(1),
      &        " nodes",nodes
 ctime            call flush(iout)
             write (iout,*) "remd_m(1)",remd_m(1)
+#endif
             do irr=1,remd_m(1)
                i=ifirst(iran_num(1,remd_m(1)))
+#ifdef DEBUG
              write (iout,*) "i",i
+#endif
 ctime             call flush(iout)
 
              do ii=1,nodes-1
 
+#ifdef DEBUG
               write (iout,*) "i",i," nupa(0,i)",int(nupa(0,i))
+#endif
              if(i.gt.0.and.nupa(0,i).gt.0) then
               iex=i
 c              if (i.eq.1 .and. int(nupa(0,i)).eq.1) then
diff --git a/source/unres/src_MD/MREMD.o b/source/unres/src_MD/MREMD.o
new file mode 100644
index 0000000..0f920c5
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diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort
index e33762c..3ca0bb3 100644
--- a/source/unres/src_MD/Makefile_MPICH_ifort
+++ b/source/unres/src_MD/Makefile_MPICH_ifort
@@ -44,7 +44,7 @@ object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
         cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
         mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
         eigen.o blas.o add.o entmcm.o minim_mcmf.o \
-        MP.o compare_s1.o prng_32.o \
+        MP.o compare_s1.o prng.o \
         banach.o rmsd.o elecont.o dihed_cons.o \
         sc_move.o local_move.o \
         intcartderiv.o lagrangian_lesyng.o\
diff --git a/source/unres/src_MD/add.o b/source/unres/src_MD/add.o
new file mode 100644
index 0000000..c13bb08
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diff --git a/source/unres/src_MD/arcos.o b/source/unres/src_MD/arcos.o
new file mode 100644
index 0000000..8a850c9
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diff --git a/source/unres/src_MD/banach.o b/source/unres/src_MD/banach.o
new file mode 100644
index 0000000..be285dd
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diff --git a/source/unres/src_MD/blas.o b/source/unres/src_MD/blas.o
new file mode 100644
index 0000000..9f988e0
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diff --git a/source/unres/src_MD/bond_move.o b/source/unres/src_MD/bond_move.o
new file mode 100644
index 0000000..945d517
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diff --git a/source/unres/src_MD/cartder.o b/source/unres/src_MD/cartder.o
new file mode 100644
index 0000000..64bd60c
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diff --git a/source/unres/src_MD/cartprint.o b/source/unres/src_MD/cartprint.o
new file mode 100644
index 0000000..855db88
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diff --git a/source/unres/src_MD/chainbuild.o b/source/unres/src_MD/chainbuild.o
new file mode 100644
index 0000000..fbe8055
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diff --git a/source/unres/src_MD/check_bond.o b/source/unres/src_MD/check_bond.o
new file mode 100644
index 0000000..2c09d2b
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diff --git a/source/unres/src_MD/check_sc_distr.o b/source/unres/src_MD/check_sc_distr.o
new file mode 100644
index 0000000..c6b399b
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diff --git a/source/unres/src_MD/checkder_p.o b/source/unres/src_MD/checkder_p.o
new file mode 100644
index 0000000..9eaf7f0
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diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
index d3e68f7..63ead23 100644
--- a/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@ -1,10 +1,10 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 5 38
+C 2 5 54
       subroutine cinfo
       include 'COMMON.IOUNITS'
       write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 38'
-      write(iout,*)'compiled Mon Apr  2 08:28:34 2012'
+      write(iout,*)'Version 2.5 build 54'
+      write(iout,*)'compiled Sun May 13 01:59:53 2012'
       write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
diff --git a/source/unres/src_MD/cinfo.o b/source/unres/src_MD/cinfo.o
new file mode 100644
index 0000000..fe53af4
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diff --git a/source/unres/src_MD/compare_s1.o b/source/unres/src_MD/compare_s1.o
new file mode 100644
index 0000000..8025089
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diff --git a/source/unres/src_MD/compinfo b/source/unres/src_MD/compinfo
new file mode 100755
index 0000000..06263ff
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diff --git a/source/unres/src_MD/contact.o b/source/unres/src_MD/contact.o
new file mode 100644
index 0000000..503f772
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diff --git a/source/unres/src_MD/convert.o b/source/unres/src_MD/convert.o
new file mode 100644
index 0000000..7ad943e
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diff --git a/source/unres/src_MD/cored.o b/source/unres/src_MD/cored.o
new file mode 100644
index 0000000..9b880d0
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diff --git a/source/unres/src_MD/dihed_cons.o b/source/unres/src_MD/dihed_cons.o
new file mode 100644
index 0000000..b49de80
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diff --git a/source/unres/src_MD/djacob.o b/source/unres/src_MD/djacob.o
new file mode 100644
index 0000000..06351ba
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diff --git a/source/unres/src_MD/econstr_local.o b/source/unres/src_MD/econstr_local.o
new file mode 100644
index 0000000..7afec0f
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diff --git a/source/unres/src_MD/eigen.o b/source/unres/src_MD/eigen.o
new file mode 100644
index 0000000..7f0b6a0
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diff --git a/source/unres/src_MD/elecont.o b/source/unres/src_MD/elecont.o
new file mode 100644
index 0000000..ba5f169
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diff --git a/source/unres/src_MD/energy_p_new-sep_barrier.o b/source/unres/src_MD/energy_p_new-sep_barrier.o
new file mode 100644
index 0000000..85a496d
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diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index e3f2c36..e3c154e 100644
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -4239,49 +4239,90 @@ C iii and jjj point to the residues for which the distance is assigned.
           iii=ii
           jjj=jj
         endif
-cd        write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj
+c        write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
+c     &    dhpb(i),dhpb1(i),forcon(i)
 C 24/11/03 AL: SS bridges handled separately because of introducing a specific
 C    distance and angle dependent SS bond potential.
         if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
           call ssbond_ene(iii,jjj,eij)
           ehpb=ehpb+2*eij
 cd          write (iout,*) "eij",eij
+        else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+          dd=dist(ii,jj)
+          if (dhpb1(i).gt.0.0d0) then
+            ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+            fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c            write (iout,*) "beta nmr",
+c     &        dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+          else
+            dd=dist(ii,jj)
+            rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+            waga=forcon(i)
+C Calculate the contribution to energy.
+            ehpb=ehpb+waga*rdis*rdis
+c            write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+            fac=waga*rdis/dd
+          endif  
+          do j=1,3
+            ggg(j)=fac*(c(j,jj)-c(j,ii))
+          enddo
+          do j=1,3
+            ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+            ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+          enddo
+          do k=1,3
+            ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+            ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+          enddo
         else
 C Calculate the distance between the two points and its difference from the
 C target distance.
-        dd=dist(ii,jj)
-        rdis=dd-dhpb(i)
+          dd=dist(ii,jj)
+          if (dhpb1(i).gt.0.0d0) then
+            ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+            fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c            write (iout,*) "alph nmr",
+c     &        dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+          else
+            rdis=dd-dhpb(i)
 C Get the force constant corresponding to this distance.
-        waga=forcon(i)
+            waga=forcon(i)
 C Calculate the contribution to energy.
-        ehpb=ehpb+waga*rdis*rdis
+            ehpb=ehpb+waga*rdis*rdis
+c            write (iout,*) "alpha reg",dd,waga*rdis*rdis
 C
 C Evaluate gradient.
 C
-        fac=waga*rdis/dd
+            fac=waga*rdis/dd
+          endif
 cd      print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
 cd   &   ' waga=',waga,' fac=',fac
-        do j=1,3
-          ggg(j)=fac*(c(j,jj)-c(j,ii))
-        enddo
+            do j=1,3
+              ggg(j)=fac*(c(j,jj)-c(j,ii))
+            enddo
 cd      print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
 C If this is a SC-SC distance, we need to calculate the contributions to the
 C Cartesian gradient in the SC vectors (ghpbx).
-        if (iii.lt.ii) then
+          if (iii.lt.ii) then
           do j=1,3
             ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
             ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
           enddo
-        endif
+          endif
 cgrad        do j=iii,jjj-1
 cgrad          do k=1,3
 cgrad            ghpbc(k,j)=ghpbc(k,j)+ggg(k)
 cgrad          enddo
 cgrad        enddo
-        do k=1,3
-          ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
-          ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
-        enddo
+          do k=1,3
+            ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+            ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+          enddo
         endif
       enddo
       ehpb=0.5D0*ehpb
diff --git a/source/unres/src_MD/energy_p_new_barrier.o b/source/unres/src_MD/energy_p_new_barrier.o
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diff --git a/source/unres/src_MD/randgens.o b/source/unres/src_MD/randgens.o
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diff --git a/source/unres/src_MD/rattle.o b/source/unres/src_MD/rattle.o
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diff --git a/source/unres/src_MD/readpdb.o b/source/unres/src_MD/readpdb.o
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diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 6ce9ec3..08d4125 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -44,7 +44,8 @@ C Print restraint information
      &write (iout,'(a,i5,a)') "The following",nhpb-nss,
      & " distance constraints have been imposed"
       do i=nss+1,nhpb
-        write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
+        write (iout,'(3i6,i2,3f10.5)') i-nss,ihpb(i),jhpb(i),
+     &     ibecarb(i),dhpb(i),dhpb1(i),forcon(i)
       enddo
 #ifdef MPI
       endif
@@ -2475,21 +2476,29 @@ c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
         endif
       enddo 
       do i=1,ndist_
-        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+     &     ibecarb(i),forcon(nhpb+1)
         if (forcon(nhpb+1).gt.0.0d0) then
           nhpb=nhpb+1
-          dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+          if (ibecarb(i).gt.0) then
+            ihpb(i)=ihpb(i)+nres
+            jhpb(i)=jhpb(i)+nres
+          endif
+          if (dhpb(nhpb).eq.0.0d0) 
+     &       dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+        endif
+      enddo
 #ifdef MPI
-          if (.not.out1file .or. me.eq.king)
-     &    write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
-     &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
-#else
-          write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
-     &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+      if (.not.out1file .or. me.eq.king) then
 #endif
-        endif
+      do i=1,nhbp
+          write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
+     &     i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
       enddo
       call flush(iout)
+#ifdef MPI
+      endif
+#endif
       return
       end
 c-------------------------------------------------------------------------------
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