Lipid data set fitting | JH | MT (in chat): Haven’t gotten to it but the conversion from existing QCArchive datasets - either opt or torsion drive datasets - to YAMMBS/YDS is on my plate right now MT (in chat): These refits are “only” valence parameters, correct? JH: yes DM: guessing that this might not really affect diffusion coefficients, is there any particular reason it would? JH: there’s an AMBER paper from 2017 where the C-C-C angle was re-fit for more flexibility and that increased diffusion in lipid tails DM: how big were you looking? JH: pentane to pentadecane
DM: with your MSD plots, I wonder if OpenFF 2.0 non-bonded re-fits made things too sticky LW – Possible, hard to say without doing a refit. JH, when you first precented this work, you showed using amber changes swapped in. Maybe try vdW params as well? JH – Could do that, we could follow up offline. DM – Could also try with openff-1.x vdw (which will have nonbonded params very similar to amber). JH – PF and I haven’t run any calcs using Parsley. Is the big difference between Parsley and Sage the nonbonded params? LW – Yes, it was a full refit, but the major change was in changing the nonbonded params. DM – So if using Parsley makes the lipid properties look better, that would tell us that the Sage nonbonded refit messed things up, maybe by making them too sticky.
JW (in chat): Brent’s Lipidmaps dataset is >95% done, working through some (hopefully) technical issues now but we’re not sure how long it will take to finish. Probably mostly usable in its current state though (modulo needing to re-export it once we complete the remaining jobs) JH – maybe the partial completion was the cause of my issues. JW: I would be surprised if that was the problem, many of our historical datasets are <100% complete JH – Would this be worthwhile to benchmark against? LW – Some knowledge about the exact composition lost with BW. But this dataset is intended to contain at least fragments of important lipids. README scripts should help explain composition and purpose. JH – Ok, I’ll check these out.
LW – TDs might be supported in YAMMBS directly now. Can discuss more offline. JH – That’d be helpful. Are there other lipid-like TD datasets I could use for benchmarking? My only one right now is the training set. LW – Not aware off the top of my head, it couldn’t hurt to check TD profiles against the training set anyway.
JR – So you have a charged headgroup and an alkane tail - Do you have counterions in simulations?
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Evaluator pre-equilibration | LW | MS – Worth noting that triethanolamine has a huge viscosity, so this is a very challenging case. MS – Might some of these systems be phase-separating? Maybe packing at a higher density might avoid this issue by removing bubbles or something? PB – Can you check whether ex. GROMACS gives the same equilibration behavior? Could be further misbehavior by openMM’s barostat. LW – Could check this. Does GROMACS have montecarlobarostat implemented? MS – Pascal Merz and my PR to add it is still waiting. DM – Different barostats may still give useful info - like if it’s an order of magnitude faster there may be something wrong wtih OpenMM’s barostat.
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