Adjust plain MD simulation PDB writing & production step counter

[IAlibay]

Fixes #1291

This PR does two things:

• Make it so that PDBs are written with the same periodicity shift as the XTC file
• Make it so that the step counter resets to 0 during the production phase. This is partly to ensure that the XTC writing is predictable but also a QoL improvement for the simulation log file (since it otherwise starts from a high number and it's unclear to users what's going on).

Checklist

• Added a news entry

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/.

[IAlibay]

Note: this PR depends on #1294

[codecov]

Codecov Report

Attention: Patch coverage is 76.47059% with 8 lines in your changes missing coverage. Please review.

Project coverage is 92.57%. Comparing base (8963fd2) to head (e793057).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...fe/tests/protocols/openmm_md/test_plain_md_slow.py	20.00%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1302      +/-   ##
==========================================
- Coverage   92.63%   92.57%   -0.07%     
==========================================
  Files         143      143              
  Lines       10957    10975      +18     
==========================================
+ Hits        10150    10160      +10     
- Misses        807      815       +8     

Flag	Coverage Δ
fast-tests	92.57% <76.47%> (-0.07%)	⬇️

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[hannahbaumann]

Thanks @IAlibay , that looks good to me! Only thing I was wondering is that if the user doesn't want waters in the traj, if it would still be useful to save a full system for the final frame.

[mikemhenry]

Does this method belong in some base class we have in utils file for our openmm based protocols?

[IAlibay]

Eventually I think, but we'll leave that for the "big refactor".

[mikemhenry]

Thanks @IAlibay , that looks good to me! Only thing I was wondering is that if the user doesn't want waters in the traj, if it would still be useful to save a full system somewhere. But maybe if the user specifies 'no water' that's what you get?

So a user sets what they want to store, are you thinking about a case where after a simulation is over, they might change their mind?

[IAlibay]

Thanks @IAlibay , that looks good to me! Only thing I was wondering is that if the user doesn't want waters in the traj, if it would still be useful to save a full system somewhere. But maybe if the user specifies 'no water' that's what you get?

I'm not 100% sure what you mean here @hannahbaumann

Is this an enhancement request to save a fully solvated PDB of the system too (I thought we were already doing that with preminimized_structure) or did we use to save a fully solvated PDB and we're no longer doing this here?

(I assume you don't mean a fully solvated XTC file).

[github-actions]

No API break detected ✅

[hannahbaumann]

Is this an enhancement request to save a fully solvated PDB of the system too (I thought we were already doing that with preminimized_structure) or did we use to save a fully solvated PDB and we're no longer doing this here?

I meant a fully solvated last frame of the MD, in case people want to use the MD protocol to equilibrate before running FEP, but not want to save big trajectories.