Add appropriate acknowledgements to PERSES and openmmtools contributors

[apayne97]

Since significant chunks of the code (~thousands of lines) in this repo are copy-pasted from https://github.com/choderalab/perses (and some bits from https://github.com/choderalab/openmmtools), which constitutes a ton of hard work from graduate students and software engineers not directly a part of OpenFE, I strongly think that more effort should be put into acknowledging these efforts. In particular, I think it would be appropriate to include:

Chodera Lab PhD Students & Post-docs: @zhang-ivy @dominicrufa @andrrizzi @Lnaden @hannahbrucemacdonald @pgrinaway

Software Scientists: @ijpulidos @mikemhenry

At a minimum, putting on the "front page" that this work is indebted to both of those code bases would be a step in the right direction. (edited for friendliness)

Thanks!

[mikemhenry]

We can certainly highlight our use of perses on our README. Longer term we will be moving the protocols out of this repo into their own. This work is in progress here https://github.com/choderalab/feflow

All the perses source code that has been adapted (the OpenFE team did refactor and clean up the code) includes a note on where it came from, so it is clear in the code where things came from. I realize that only a fraction of the people who use the software read the code, but had we imported perses instead of refactor/cleanup + vendor the code, we would be in the same situation.

We are working on adding duecredit support so that every package that gets used can get a proper citation. Since users can mix and match different parts of the pipeline, we need a way to automatically handle that.

We don't vendor anything from openmmtools but do import the package. OpenFE hasn't published any papers yet but please be assured that openmm, openmmtools, perses, and any other software packages we use will be cited appropriately.

[IAlibay]

We've been lacking on getting duecredit up and going, I'm so sorry about that. Let me see if I can get at least a PR up this afternoon.

[richardjgowers]

Hey @apayne97 just to add some context. We've been working with @jchodera and the perses team on the above. The long term plan has been to temporarily vendor in some code, do some refactoring/etc, then push this back out as a separate, properly attributed/acknowledged package which we depend on. Logistically this allowed both the two development teams to move fast.

I'll admit the current halfway state hasn't been communicated well to people not involved in the process and lacks the proper attribution. We'll work on fixing this up in the coming days.

[apayne97]

Thanks for highlighting the work you've been doing on this! It does seem like most of the "damage" was done by people not directly involved, and I think if OpenFE was just another small lab effort it might not be such a big deal, but with all the OMSF and OpenFE stuff getting "press" in our field it makes it a bigger deal. Glad to see the PR go up!