Fix perturbation to Verlet scheme when not perturbing

A .top that has B-state parameters for non-bonded interactions
should run the same with free-energy = no as a .top that has no
B-state parameters. Renamed variable to better reflect its use,
and used it to correctly trigger the FEP code path.

Change-Id: I47656b29ef4ca2462af0fb587e0424d0eab3d5c4