Merge branch 'master' into rotation

Conflicts:
	src/kernel/runner.c

diff --cc src/gmxlib/names.c
Simple merge

diff --cc src/kernel/CMakeLists.txt
Simple merge

diff --cc src/kernel/Makefile.am
Simple merge

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

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

diff --cc src/kernel/runner.c
index 94621948f2ef42e3a363715daffe7ff450863e98,aaef7ab0b41c59cbf2d02346b7a2c7ebb66fee87..a328fbf75a65d9d76c53381a3d37afc8749fe609
--- 1/src/kernel/runner.c
--- 2/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@@ -52,6 -52,6 +52,7 @@@
  #include "mdrun.h"
  #include "network.h"
  #include "pull.h"
++#include "pull_rotation.h"
  #include "names.h"
  #include "disre.h"
  #include "orires.h"

diff --cc src/mdlib/mdebin.c
Simple merge

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