Fix issue #319 #320
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Fix issue #319 #320
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This PR fixes #319 by resetting the internal step counter of the dynamics object when a NaN crash occurs. Previously this was not reset, so that the time stamp for energy and trajectory frames would get out of sync following a crash. This problem is amplified when running repex since OpenMM state is swapped between replicas, meaning the internal clock for a replica could get changed following an exchange.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Tagging @akalpokas