Update RE-EDS PyGromosTools

[RiesBen]

The RE-EDS repository of the rinikerlab is stuck on an old ... very old PyGromosTools version. I think we should update it, so the RE-EDS project can benefit from new developments of PyGromosTools!

[candidechamp]

I can take care of making RE-EDS come back to a newer version of PyGromos (version 3 when it is out).

I discussed with Marc today that it would be good to add all of our ideas related to this code update here so here is why I have so far:

• Modify the way a post job analysis converts the trc file into a pandas DataFrame with all coordinates as this takes far too much space (and leads to an error) when working with protein trajectories. Ideally, it would be good to add an option to create a binary format trajectory (e.g., .dcd or .xtc) such that the trajectory can be imported in common python MD analysis tools (MDtraj, MDAnalysis, etc., etc.)