[WIP] Do an MD pre-equilibration for AFE simulations

[IAlibay]

Fixes #612

TODO:

• Add user settings for the pre-equilibration
• Write out an XTC file or similar?
• Test on a few systems locally

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[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2023-11-15 17:52:39 UTC

[IAlibay]

I'm wondering if we could modularize the "run a simulation" part of #516 so this could just be imported here? Looking at the TODO items, seems like I'll just end up copying what @hannahbaumann already wrote.

[richardjgowers]

Yeah if that just defined an MDUnit then either protocol could issue that in their DAGs

[IAlibay]

Short term I'd probably not look to break this up into more units, there's a ton of "half way" stuff by this point which we would need to serialise out and throw across units, that's a pain right now - probably post 1.0.

Maybe to explain the short term need here - this is something I need for the ABFE stuff.

maybe the answer is to just go as-is with the code duplication and clean up later?

[codecov]

Codecov Report

Attention: 72 lines in your changes are missing coverage. Please review.

Comparison is base (7a39491) 92.21% compared to head (5eadd6d) 91.24%.
Report is 4 commits behind head on main.

Files	Patch %	Lines
openfe/tests/protocols/test_openmm_afe_slow.py	25.39%	47 Missing ⚠️
openfe/protocols/openmm_afe/base.py	26.66%	11 Missing ⚠️
...protocols/openmm_afe/equil_solvation_afe_method.py	60.00%	8 Missing ⚠️
openfe/protocols/openmm_rfe/equil_rfe_methods.py	57.14%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #614      +/-   ##
==========================================
- Coverage   92.21%   91.24%   -0.97%     
==========================================
  Files         124      125       +1     
  Lines        8594     8478     -116     
==========================================
- Hits         7925     7736     -189     
- Misses        669      742      +73     

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[richardjgowers]

@IAlibay do you want me to finish this up or is it obsolete now?

[IAlibay]

@richardjgowers I'm working on this elsewhere - this doesn't need handover.

[IAlibay]

Superseded by #720