Do we need to make sure we're using this everywhere we write out parameters? I see we use it for the atom mass, but not anywhere else.

Yep, for in order to handle any input unyts this will do the filtering. I was just too lazy to do it every time at first. Was wondering if you think we should make a system that isn't specific to LAMMPS for this one. It is the exact same as the real units, but maybe a touch confusing to copy them across to other engines. What do you think?

I wonder if unit_system should be a parameter of write_prm that defaults to None. If nothing is passed, then all units are used as-is from the toplogy? If we set unit_system = topology.unit_system as default behavior, would that work as well?

def write_prm(topology, filename, unit_system=None):
    if not unit_system:
        unit_system = topology.unit_system

The PRM file looks to me like it has default assumed units of kCal/mol, angstrom, amu, radians, etc for it's units. So it can only convert to one defined system.

This doesn't need to be fixed here, but I feel like this attribute should be more readable rather than just knowing that 0th index is LJ and 1st index is electrostatics. Maybe a dict? I can open a separate issue.

Was thinking the same thing myself. I think it should also be {"electrostatics":{"1-4":0.5}}, instead of a fixed list. Could potentially be some odd 1-5 interactions at some point.

Yeah, that's sort of what I was thinking as well.