Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6

Conflicts:
	CMakeLists.txt

Change-Id: I67d65e260f68442841d8b901d77780b8d1505340

diff --cc CMakeLists.txt
index 7c1229f2b1676eef01def9aad743fdd18f45cc1c,086b798036cf7056e0ce95e9397007afa05d1a56..8653d21c0d688bae7b1747af311f107d3719448b
--- 1/CMakeLists.txt
--- 2/CMakeLists.txt
+++ b/CMakeLists.txt
@@@ -1,4 -1,6 +1,6 @@@
 -cmake_minimum_required(VERSION 2.6)
 +cmake_minimum_required(VERSION 2.8)
+ # Keep CMake suitably quiet on Cygwin
+ set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
  
  project(Gromacs)
  include(Dart)

diff --cc src/kernel/gen_ad.c
Simple merge

diff --cc src/kernel/pdb2top.c
index 7d09edc2f200fa0bb7eb864dbcfff1177fc418e3,98b5d13347601f7353edcff672f91b28219ce2f5..ca2f0ca61d50b774b532fa30d4549cdae678fa79
--- 1/src/kernel/pdb2top.c
--- 2/src/kernel/pdb2top.c
+++ b/src/kernel/pdb2top.c
@@@ -737,9 -739,15 +740,9 @@@ static void do_ssbonds(t_params *ps,t_a
    }
  }
  
 -static gmx_bool inter_res_bond(const t_rbonded *b)
 -{
 -    return (b->AI[0] == '-' || b->AI[0] == '+' ||
 -            b->AJ[0] == '-' || b->AJ[0] == '+');
 -}
 -
  static void at2bonds(t_params *psb, t_hackblock *hb,
-                      int natoms, t_atom atom[], char **aname[], 
-                      int nres, rvec x[], 
+                      t_atoms *atoms,
+                      rvec x[],
                       real long_bond_dist, real short_bond_dist,
                       gmx_bool bAllowMissing)
  {

diff --cc src/kernel/pgutil.c
Simple merge

diff --cc src/tools/gmx_energy.c
Simple merge

diff --cc src/tools/gmx_msd.c
Simple merge