Peptide and GB3 benchmarks in OPC water  | @Chapin Cavender | Slides will be uploaded Meeting is recorded Slide 7: error bar is confidence interval that comes from standard error Slide 8: aside from Val3, OPC generally improves results for SMIRNOFF Slide 9: Slide 10: WS: this looks great. TIP3P has an unrealistically large diffusion constant – I’ll bet OPC is much closer to experiment, so maybe kinetics are slower, so anything crazy might take longer to happen LPW: what are you looking at? CC: recommend using OPC from now on MS: what about tip4p-fb and other four-point models? Others may also balk at extra computational cost CC: good point MS: want to do subset of mixture properties with a bunch of water models. OM is gone, LW has other work to do, maybe I can find someone in my group to do it. e.g. Anika BS: agree that’s a great idea MS: enthalpies of mixing, densities that involve water, transfer solvation energies. Maybe can coordinate with LW to see how much there is to do. MS and Lily can coordinate CC: can repeat with tip4p-fb since we already have the port in SMIRNOFF LPW: the parameters between OPC and TIP4P-FB are very different. Similarly, OPC3 vs TIP3P-FB are very similar. LPW: could see if you could reproduce tipxp-fb in evaluator with tipxp data set, then add mixture properties MS: I think we can test water models before we re-fit models JW: wrt virtual sites, OpenFE may not have infrastructure to roll out virtual sites for a while. We may not be able to easily do FE calcs with four-site models. CC: we thought we would wait until release candidate to do protein-ligand benchmarks, which will be when I hand off to Lily for refit MS: we don’t want to do PLBs until we are comfortable about protein stability JW: i’ll keep them up to date and ask when they may have vsites implemented BS: I thought OpenFE discussion was to do with vsites on ligands, not water model JW: I think water model might be a bit simpler. In my understanding, the difficulty is with alchemical transformation bookkeeping. MS: if vsite has no charge on it, the statistical mechanics are identical as if there’s no vsite DLM: from OpenMM POV, it should just be a matter of running with the water model, whichever one it is. Unless they’ve done something really weird, it should be quite simple MS: since water model isn’t changing, yes, it should be fairly simple BS: agree JW: I’m just being cautious in case OpenFE can’t handle it DLM: worth putting on their radar (general agreement 4-site water should be straightforward)
CC: summarise to do: Run benchmarks with tip4p-fb MS will see if someone can run small molecule properties MS: won’t be before OpenFF meeting, so let’s nail the plans down at the meeting in a week. We can aim for results at end of May. Maybe Tim could do it CC: we can use these results to decide further protein benchmarks DLM: can use agenda on Monday to figure this out
MS will sync up with Lily to figure out what properties to use CC will sync up with LPW about couplings
Update on AF: MS: on Monday is when we have updated NIH information MS: we can put a list of accepted publications. Anything that’s been accepted in the past two months? Sage Owen’s surrogate model
MS: covid regulations still in place, so we can submit up to 1 page of preliminary data Since our results are middling, not sure this is the best idea. Should we try to show tentative results? Consensus: don’t submit tentative results
CC: thanks JW and MT for helping with OPC! MT: TIP4P (EW and FB variants) are not in the forcefields repo but the work is done, just needs a review/merge/release when that’s important
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