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Update topology/system particle bookkeeping in OpenMM #3815

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Update topology/system particle bookkeeping in OpenMM

Update topology/system particle bookkeeping in OpenMM #3815

Test on macos-12, Python 3.11, OpenMM true, Pydantic 2, OpenEye true

Test on macos-12, Python 3.11, OpenMM true, Pydantic 2, OpenEye true
succeeded Sep 18, 2024 in 14m 35s