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Update topology/system particle bookkeeping in OpenMM #2487

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Update topology/system particle bookkeeping in OpenMM

Update topology/system particle bookkeeping in OpenMM #2487

Run time

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Job Run time
test (ubuntu-latest, 3.10)
22m 4s
test (macos-12, 3.10)
53m 16s
1h 15m 20s