Fixes for md-vv and rerun

Implements several fixes for md-vv and mdrun -rerun.

* Dispersion is correctly added.
* COM motion is removed only on the second half of the timestep.
* Now can do md-vv rerun with multiple threads.
* Now gives exact kinetic energy reruns for everything except MTTK, where the iterative algorithm
makes exact kinetic energy impossible when nstpcouple == 1.
* Eliminated an extranaous variable in anderdsen temperature control since I had to move that code anyway.

Change-Id: I1c2a5a9c3da549baa0ef25601bc623a3e39bff84
Merge "Fixes for md-vv and rerun" into release-4-6