fixing rerun with free energy + .xtc or .gro

When running rerun specifying init-fep-state rather than lambda (which
is necessary if the vector components are specified separately), the
init-fep-state in the .mdp is ignored. There .trr appears to already work
correctly.

Fixes bug #1240

Change-Id: Id118ae9273ef67438797306a74ac3bccfb8c4dba
Merge "fixing rerun with free energy + .xtc or .gro" into release-4-6