Merge branch 'prerelease-3.2.1' into czarek

Conflicts:
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	source/unres/src_MD/cinfo.f
	source/unres/src_MD/energy_p_new_barrier.F

diff --cc bin/unres/MD/unres_ifort_MPICH_GAB.exe
index 97d45b7,a5decdb..968912a
Binary files differ

diff --cc source/unres/src_MD/cinfo.f
index 3f50f77,7534dcb..07a66c9
--- 1/source/unres/src_MD/cinfo.f
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,10 -1,10 +1,10 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
- C 3 1 52
 -C 3 1 78
++C 3 1 53
        subroutine cinfo
        include 'COMMON.IOUNITS'
        write(iout,*)'++++ Compile info ++++'
-       write(iout,*)'Version 3.1 build 52'
-       write(iout,*)'compiled Sun Feb 17 00:55:22 2013'
 -      write(iout,*)'Version 3.1 build 78'
 -      write(iout,*)'compiled Sun Feb 17 03:00:27 2013'
++      write(iout,*)'Version 3.1 build 53'
++      write(iout,*)'compiled Sun Feb 17 03:17:55 2013'
        write(iout,*)'compiled by czarek@piasek3'
        write(iout,*)'OS name:    Linux '
        write(iout,*)'OS release: 2.6.32-42-generic '

diff --cc source/unres/src_MD/energy_p_new_barrier.F
index 102862a,64dd328..0af23e5
--- 1/source/unres/src_MD/energy_p_new_barrier.F
--- 2/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@@ -4279,13 -4279,14 +4279,13 @@@ C 24/11/03 AL: SS bridges handled separ
  C    distance and angle dependent SS bond potential.
  cmc        if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
  C 18/07/06 MC: Use the convention that the first nss pairs are SS bonds
- c          if (.not.dyn_ss .and. i.le.nss) then
- C 15/02/13 CC dynamic SSbond
-         if (.not.dyn_ss.and.
-      &   ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then 
+         if (.not.dyn_ss .and. i.le.nss) then
+ C 15/02/13 CC dynamic SSbond - additional check
+          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
- c          write (iout,*) "eij",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)

diff --cc source/unres/src_MD/geomout.F
Simple merge

diff --cc source/unres/src_MD/readrtns.F
Simple merge