Change get_simsteps function to handle NVT equilibration in plain MD protocol

[hannahbaumann]

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[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/protocols/openmm_utils/settings_validation.py:

Line 68:17: E222 multiple spaces after operator

• In the file openfe/tests/protocols/test_openmmutils.py:

Line 45:80: E501 line too long (80 > 79 characters)

Comment last updated at 2023-11-22 14:33:35 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (d011065) 90.97% compared to head (c45f85a) 90.97%.
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #647      +/-   ##
==========================================
- Coverage   90.97%   90.97%   -0.01%     
==========================================
  Files         127      127              
  Lines        8679     8675       -4     
==========================================
- Hits         7896     7892       -4     
  Misses        783      783              

Flag	Coverage Δ
fast-tests	90.97% <100.00%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[IAlibay]

@hannahbaumann could you tick that box re: certifying contributions?

[IAlibay]

Couple of quick things to change, otherwise this looks good.

[IAlibay]

This is great, de-hardcoding re-usable methods is super useful!

[hannahbaumann]

@IAlibay : Addressed your comments! I realized that a lot of tests are failing in the plain MD PR because I had already changed the get_sim_steps function for the plain MD protocol, so the RFE and HFE tests are failing, probably best to fix/merge after this merge?!

[IAlibay]

lgtm!