Ivy Zhang

It would also be good to include the Zenodo software citation, and dominic's and my papers as ways to cite Perses. Perses 0.10.1 citation (may need to generate new citations...

I think we already sped things up a bit using this PR: https://github.com/choderalab/perses/pull/1065 There may be room for more speed up, but I think its fine for now. What do...

@ijpulidos @mikemhenry : The first thing I would do to fix these failing tests is to increase the number of steps per iteration to 250 (as we discussed [earlier](https://github.com/choderalab/perses/pull/1065#issuecomment-1244367915)) If...

It might be best to run these locally (on lilac or your external GPU) first to make sure you can get the tests to converge with the changes I recommended

~@ijpulidos : Can you try running the small molecule tests even longer (5 ns)? If they are still failing even with 5000 iterations, there may be a more significant problem...

Ah actually ignore my above comment, I think you're right that we should change the tests to use phenol to paracetamol. But not sure which transformation to use for the...

I can review this later tonight or tomorrow! Please wait to merge. Thanks!

Reviewing this now. Github won't let me comment on lines that haven't been changed, but I noticed that [this line](https://github.com/choderalab/perses/pull/1065/files#diff-b79cc8cc86e56e993941143d09e09959413d8caf120e67610d6f3064031718d0R13): "Note: We are using 50 steps per iteration here to...

Closing this since for protein mutations, we decided to map all backbone atoms and sidechain atoms up to the beta carbon

Closing this, since we did not observe that this addressed our sampling problems.