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HT slides | Post slides here Discussion of workflow: Data sharing - If working with Shirts lab, can’t share structures since there’s IP protection. Maybe come up with similar molecules that can be publicly reported for debugging? JW – Proposal - Use RDKit reactions to construct polymer, generate conformer using RDKit, load into openFF using from_rdkit, (possibly use packmol wrapper in Interchange to construct simulation box) use nagl to charge, simulate. MM – Interested in participating in validation? Want to compare different charge models etc. JW – Not interested in validation but Lily Wang would be. Charge models I can think of would be Nagl and Espaloma for whole-molecule, or for constructing librarycharges Antechamber AM1BCC, RESP (OpenFF has an ugly solution for this, I can point you to this if you run out of other options), and maybe an XTB charge model (if that exists?)
JW – Happy to help put together a prototype to go from polymer definitions → simulation at any point. Let me know if I can help with a screenshare, or work on a prototype.
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