Add box vector fix to AFE base

[IAlibay]

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/.

[codecov[bot]]

Codecov Report

:x: Patch coverage is 66.66667% with 2 lines in your changes missing coverage. Please review. :white_check_mark: Project coverage is 92.73%. Comparing base (0bd14c7) to head (9cbf7aa). :warning: Report is 274 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_afe/base.py	66.66%	2 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1275      +/-   ##
==========================================
- Coverage   94.34%   92.73%   -1.62%     
==========================================
  Files         141      141              
  Lines       10858    10858              
==========================================
- Hits        10244    10069     -175     
- Misses        614      789     +175     

Flag	Coverage Δ
fast-tests	92.73% <66.66%> (?)
slow-tests	?

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[CurtisColwell]

I am testing this branch and it has so far completely resolved the problem I was facing (https://github.com/OpenFreeEnergy/openfe/discussions/1259)

So far it has been 6 successful ASFE calculations with default settings.

[IAlibay]

I am testing this branch and it has so far completely resolved the problem I was facing (#1259)

So far it has been 6 successful ASFE calculations with default settings.

Amazing, thanks so much for testing this out!

[github-actions[bot]]

No API break detected ✅

[IAlibay]

Forgot to add a new entry, will follow up.