Making higher-level morphology of whole system (nanoparticle vs. gel etc)
MM+HT – Several options here. Could use Shirts lab tools for polymer building but some limitations around branching/arbitrary consistencies. Could use ambertools/tleap with custom monomers.
JW – May be good to do “quick and dirty” implementation initially to get an understanding of problem domain, and then plan to refactor each year as the parameters become more known.
Data sharing - If working with Shirts lab, can’t share structures since there’s IP protection.
JW – Maybe come up with similar molecules that can be publicly reported for debugging? This will be generally difficult if you can’t provide reproducing cases for bugs.
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 of several molecules) 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?). Our FFs are trained against AM1BCC charges so there’s a chance that performance would get worse with other models.
JW – OpenFF’s current FFs are trained against TIP3P water.
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.