Check for bugs / consistent / expected behavior in specified steps versus trajectory output

[eirrgang]

We need clearly defined behavior relating the simulation steps specified in a TPR file, parameters that may or may not be specified as overridden by a user, and the current files or artifacts for checkpoint data and trajectory outputs. If we find cases where behavior in some scenarios is not clearly specified for the core GROMACS or CLI, or cases where the observed behavior in the upstream GROMACS repo seems to differ from the specified behavior, we should be sure to file bug reports and/or seek clarification so that all users get the behavior they expect.

In particular resuming from a checkpoint that was produced with TPR MDP options overridden may be poorly specified. For instance, we should re-check what the GROMACS 2019 candidate does when a checkpointed trajectory has already gone past the end of the specified trajectory.