Print out atom numbers in g_rmsf

Reasonable output of g_rmsf would be the atom numbers
and not the group indices.

Fixes #893

Change-Id: I16a8e25f1934ef40952f24ffd5ab835acabfff72
Use stat for gmx_is_file. Fix get_libdir with symlinks.

In commit 4e057440520c1 I used lstat instead of stat confusing the
two. The commit tried to fix the misidentification of directories.
There is no need to distinquish between symlinks and files (and
thus break it if a binary is a symlink).

Change-Id: Ie964e826729a35f11516fb3d002ebc01cbb7a564
Fixes #1035 NaN in g_cluster output.

Now always initializes the masses of the atoms to prevent
division by zero downstream.

Change-Id: I1b38ccc7982d4340ed068535f7b7dd8e75e1a4c4
Merge "Use stat for gmx_is_file. Fix get_libdir with symlinks." into release-4-5-patches
Minor spelling&header fixes for various man pages

see: http://patch-tracker.debian.org/patch/series/view/gromacs/4.5.5-2/31_manpages.patch

Change-Id: I813ed653b9b50125652fef5522a51304773414dc
Remove superfluous memory allocation.

The next line allocates the memory again.

Fixes #918.

Change-Id: I6f727cf059ccdc5d407b8398b9b29db625c120b8
Merge branch 'release-4-5-patches' into comp_el
Merge "Print out atom numbers in g_rmsf" into release-4-5-patches
Merge branch 'release-4-5-patches' into comp_el