MD trajectory (when using the PlainMDProtocol) does not write final frame

[IAlibay]

Just triaging this, but it looks like our trajectories don't write the final frame (something which I expect coming from GROMACS and AMBER-land).

It might be that we need to manually force writing the final frame to the XTC.

[IAlibay]

This isn't a thing in the end. Looks like it's just that we're storing PDBs without enforcePeriodicBox and the XTC reporter is.

My suggestion short term is that we enforce things in the same way for both types of files.

Longer term we might need to make this optional, I know that VMD doesn't play super well with files that have enforcePeriodicBox=True.