[WIP] Net charge support in ABFEs

[IAlibay]

Fixes: #1662

Checklist

• Added a news entry

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

[codecov]

Codecov Report

❌ Patch coverage is 75.36232% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.80%. Comparing base (80cbc22) to head (cef9cb7).

Files with missing lines	Patch %	Lines
...e/protocols/openmm_afe/equil_binding_afe_method.py	60.00%	16 Missing ⚠️
openfe/protocols/openmm_afe/base.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1614      +/-   ##
==========================================
- Coverage   95.32%   92.80%   -2.52%     
==========================================
  Files         183      183              
  Lines       15765    15803      +38     
==========================================
- Hits        15028    14666     -362     
- Misses        737     1137     +400     

Flag	Coverage Δ
fast-tests	92.80% <75.36%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅