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Perses/OpenFF/OpenFE coordination | JW – We’re trying to figure out how OpenFF, OpenFE, and perses devs can meaningfully work together. Still a lot of unknowns. We had a meeting this morning that I thought about inviting you to, but it would have been really last-minute. But I can loop you in for future meetings if you want IP – Please loop me in.
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TopologyMolecule deprecation | |
Residue perception/performance improvements from splitting at peptide bonds. | IP – Had limited time last week since I had problems with OpenMM. Some low-level CUDA things with how openmmtools context cache was possibly leaking memory. IP – Tried to speed up reading-from-PDB-and-assigning-bond-orders by splitting at peptide bonds. First attempt was to split the molecule at peptide bonds by perceiving the simple subgraph.
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