CalCraven

So there's three ways we can address the issue: 1. Quick and Dirty (ff-utils): Use the tools in the forcefield_utilities package to convert the GMSO XML to a Foyer XML...

We should potentially add in a future PR a deprecation warning for reset_index

Hi @iGulitch, sorry for the slow responses, @daico007 was actually defending his Ph.D. thesis around then, so I'm guessing that's why he didn't get back to you. I was passing...

Raise and issue about python < 3.12 though once this is merged, since we'll want to fix that when we get to that issue.

Thanks for all this info @bc118 @dyukovsm! This is really helpful having specific files and examples to work with when writing unit tests. I would say because the various water...

> I would request that the residues be a part of the atom/bead in all cases, preferably as an attribute. I outline some of the major reasons below. I agree...

In order to clarify some things on my end in regards to your fourth bullet point, is the current treatment of charges just included in the nonbonded functionals section heading?...

I think this also needs to get deprecated, as that whole module has lost it's usefulness. The replacement function is in `gmso/core/forcefield.py: ForceField.to_xml(filename)` function

> Are we naming the HarmonicTorsionPotential.json potential correctly? It seems like we should change the name or equation, or add both and change them accordingly. Thoughts? > > It seems...

> We need to ask if we want to use the Phi variable for RB torsions, as it is used for OPLS and Periodic torsions. RB torsion Phi is not...