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Update topology/system particle bookkeeping in OpenMM #2489

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Update topology/system particle bookkeeping in OpenMM

Update topology/system particle bookkeeping in OpenMM #2489

Run time

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Job Run time
test (ubuntu-latest, 3.10)
22m 59s
test (macos-12, 3.10)
44m 41s
1h 7m 40s