Remove OpenMMEngineSettings and create GromacsEngineSettings

[hannahbaumann]

Description

As these settings are not used in this protocol, we should remove them.

This PR addresses following issues:

• Add engine settings for GPU selection and pinning #29
• engine_settings should be removed as they are OpenMM specific #19

[codecov]

Codecov Report

Attention: Patch coverage is 90.47619% with 2 lines in your changes missing coverage. Please review.

Project coverage is 91.89%. Comparing base (89fadea) to head (dfaae75).
Report is 10 commits behind head on main.

Additional details and impacted files

[IAlibay]

To be discussed, ntomp really is the engine setting, you probably should have that (and controls for GPU allocation) in its own setting.

[hannahbaumann]

Maybe we could instead have a GromacsEngineSettings class?

[IAlibay]

Maybe we could instead have a GromacsEngineSettings class?

Yeah that sounds like a good idea.

[pep8speaks]

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

• In the file openfe_gromacs/protocols/gromacs_md/md_methods.py:

Line 1107:80: E501 line too long (82 > 79 characters)

Comment last updated at 2024-09-26 14:34:05 UTC

[IAlibay]

This looks good to me, could you maybe just open an issue that says something along the lines of "review engine settings for gmx mdrun"?

This is purely to make sure we remember that we'll want to review if those flags work for us after we've started using this in practice.