fixed resetting states with parallel Verlet scheme

The simulation state might need to be reset with e.g. REMD
or energy minimization. With the Verlet scheme in parallel
the contents of one outdated array was used, leading to gmx_fatal.
Fixes #1024

Change-Id: I24d07ea7dfd41e9689dd083cafbf778a7c8033fd
Merge "fixed resetting states with parallel Verlet scheme" into release-4-6