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
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 "Print out atom numbers in g_rmsf" into release-4-5-patches
Merge release-4-5-patches into release-4-6

Conflicts:
	src/kernel/readir.c (trivial)

Change-Id: I6def10cca9a25c0587694ea77a5a6f7a43ca308d