Replace all mdrun rngs with cycle based rng

The stateful random rumber generator (rng) used previously doesn't
produce reproducible results in parallel for sd/bd and doesn't
produce reproducible results for continutation for replica exchange.
The rng state has been removed from the checkpoint file.

Fixes #995

Change-Id: Id2a5d064cf363c54db3c16a0675cfeba553feeaa