Additional selection examples

Additional selection examples

Add some examples with explicit tool references, in particular for how
to use selections with tools that require pairs of atoms (gmx distance
and vector options of gmx gangle).

Add examples to explain the difference between the various
center-of-mass keywords.

Fix old note about default index groups with selection tools
(defselections.dat is not currently used).

Change-Id: Ic9e723e6dd2f46f8f0f5a7e1c4127994577acc3e