Free-energy now works with the Verlet scheme

Free-energy now works with the Verlet scheme

Implemented perturbed non-bonded interactions with the Verlet
by masking them from the nbnxn pair lists and storing them in an
old-fashioned group neighbor list. This way we keep a single
free energy kernel.
The free energy kernel uses OpenMP atomic for reductions.

Also fixed grompp setting nstcalcenergy=0 with nstenergy=0.

Change-Id: I5a6a7e84b46e06250d141e2e08cb3a11077cddab