From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Mon, 18 Feb 2013 08:04:50 +0000 (+0100)
Subject: Merge branch 'prerelease-3.2.1' into czarek
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=4dfd5a32bfb40a62c23d814ac70bfef4cc085d63;hp=-c;p=unres.git

Merge branch 'prerelease-3.2.1' into czarek

Conflicts:
	bin/unres/MD/unres_gfortran_single_GAB.exe
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	source/unres/src_MD/cinfo.f
	source/unres/src_MD/parmread.F
---

4dfd5a32bfb40a62c23d814ac70bfef4cc085d63
diff --combined bin/unres/MD/unres_ifort_MPICH_GAB.exe
index 968912a,c8defa0..0000000
deleted file mode 100755,100755
Binary files differ
diff --combined source/unres/src_MD/energy_p_new_barrier.F
index 0af23e5,2557051..d2cea5f
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@@ -1589,6 -1589,8 +1589,8 @@@
              IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
                call dyn_ssbond_ene(i,j,evdwij)
                evdw=evdw+evdwij
+               if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') 
+      &                        'evdw',i,j,evdwij,' ss'
              ELSE
              ind=ind+1
              itypj=itype(j)
@@@ -4257,8 -4259,8 +4259,8 @@@
        include 'COMMON.IOUNITS'
        dimension ggg(3)
        ehpb=0.0D0
 -cd      write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
 -cd      write(iout,*)'link_start=',link_start,' link_end=',link_end
 +c      write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
 +c      write(iout,*)'link_start=',link_start,' link_end=',link_end
        if (link_end.eq.0) return
        do i=link_start,link_end
  C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
@@@ -4286,6 -4288,7 +4288,6 @@@ C 15/02/13 CC dynamic SSbond - addition
            call ssbond_ene(iii,jjj,eij)
            ehpb=ehpb+2*eij
           endif
 -cd          write (iout,*) "eij",eij
          else if (ii.gt.nres .and. jj.gt.nres) then
  c Restraints from contact prediction
            dd=dist(ii,jj)
@@@ -4425,7 -4428,6 +4427,7 @@@ c      dscj_inv=dsc_inv(itypj
        eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
       &  +akct*deltad*deltat12+ebr
       &  +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
 +     &  +ss_depth
  c      write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
  c     &  " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
  c     &  " deltat12",deltat12," eij",eij