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Item | Notes |
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General updates | JW – Starting Friday, I’ll be mostly offline next ~2 weeks JW – Advanced biopolymer toolkit workshop pt 2: Weds morning at midnight Pacific. CC – Tea time on Tuesday afternoon at 4 PM US Pacific
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Individual updates | DN Last Thursday I had my check in with Karmen - She pointed out that there’s more that I could be doing. So I wanted to check with you all about whether I could do anything to make your life easier/if there’s anything that Karmen used to do that I could pick up doing. I’m open to input at any time. With JW’s vacation, I’d like to make sure that we keep things running for 2 weeks. So we should keep meeting notes getting taken and at a high quality. In the future I want to take more of JW’s work and help run meetings.
MT (bad connection) Interchange workshop Went well, preparation was a timesink but most objectives were met Low attendance, some engagement from live users, no offline engagement yet Event notes/debrief /wiki/spaces/MEET/pages/2438004739 Willing to help push advertising, but can’t own the communication stream myself. Would like to gather more users. JW – I think that engagement is a long-term effort. We’re building up userbase that will cross-pollinate in the field and grow massively MT – I don’t think this is an ok situation - We don’t know what people really need, and we’re developing speculatively. I also keep hearing that adoption is slow-growing but inevitable, and I’m not sure at what point it will really “happen”. DD – Do you think that having direct customer engagement is important for the health of the project? MT – Yes - I’d call it “adoption” but we probably mean the same thing. DD – I think it’s probably worth chasing these people down and developing a personal relationship. This will help you gain information about their specific needs. Gaining adoption in one partner will lead to bleed-over into other partners. MT – Understood. JW – I see it as a not great outcome if we have engineers doing external communication since this makes it hard to do focused work. But if this is a skillset you want to develop then go for it. But I’d rather have DN leading external communication. MT – I’m not sure that the org can reach adoption under the current operational model. DD – I strongly believe that unfiltered customer feedback is the best way to get adoption. Even if that means screensharing on their projects. This builds a relationship that brings benefits and candid communication in the future. MT – I think I have a hazy but somewhat useful picture of why our user adoption is lagging - I think people are waiting for Rosemary so they can do proteins and small molecules. Or there’s something that’s not directly a tooling issue (installation, documentation, etc) that’s buried here. I think that the barrier to entry is pretty low, so I’m curious as to why adoption isn’t proceeding as fast as we’d like. JW – Regarding gathering needs/reasons for slow adoptions- We’re going to be restarting the annual survey this year, and I’ll make sure to add questions about “what’s keeping you from having greater adoption?” and “would you like to work with an OpenFF dev?”
Water models Another attempt at gaining consensus on prior proposal of adding water models to openff-forcefields Failed to obtain consensus or stay on topic of decision points, bailing out PB – I thought we agreed to include water models? JW – I don’t think we agreed to do this. MT – My understanding is that we didn’t reach consensus on some major issues, and we didn’t even get to discuss several others. PB – If we’re using the same values as in a paper, where do the differences come from?
Scheduled meeting with Chodera + CCG, reschedule for this week due to another attendee cancelling Added GAFF + Interchange example
DD PB Worked on revisions to Sage manuscript. Answering some Qs like from OM - Like starting point FF was 1.3.0 instead of 1.3.1, so we’re not sure if it includes sulfonamide fix. So I used MT’s ligand-in-water example to test whether the geometry is fixed (thanks MT for the example!). A schrodinger person raised an issue on the SPICE set repo about downloading issues (the QM specification was randomly set incorrectly during download). So I set the QM specification to be hard-coded instead of “default” Started looking into BSwope’s recommendation to use energy levels as fitting target, so we could use information from optimized confs instead of just geometries for the fit. This is still a WIP. DD – More details? PB – In a FF release meeting, BSwope showed examples where ligand conformers optimize to almost the same structure in QM and MM, but their relative conformer energies are different. DD – Thanks PB – Did anyone here use the “ab initio” target in forcebalance? I know TG uses it. This sounds similar to what BSwope was asking for. DD – I might recommend talking to LPW. CC – I haven’t used it, but I think the point is to use a single-point energy, right? PB – I think TG modified this to use the optimization trajectory instead of just the optimized structure. JW – If we’re comparing rank orderings, does that give a non-smooth scoring function?
CC Submitted draft of abstract on protein FF effort for Biophysical Society Annual Meeting in February. Abstract is here: Followed up on additional chemistries (suggested by CBayly at FF Release meeting) that are assigned different torsions for chemically equivalent atoms with delocalized charge Still running protein parameter fits on TSCC, slow progress. Seems to be stuck on diagonalizing Hessian after first step for >3 days. Is this normal? PB – I recall this taking >10 steps to find… 3 days is a long time. How many workers are you using? CC – 10 workers at a time. Any more than that I get an idle timeout, since additioanl workers aren’t assigned any work. I think there’s a small number of jobs that are taking a long time and holding everything up. PB – Maybe we should do a call with TG and hear if he has any tips for speeding it up. JW – May be useful to try Simon’s inputs (without peptides) to see if the timing gets a lot faster. That would help narrow down possible causes CC – Also it’s possible that ELF10 is taking a long time CC – Doesn’t FB cache charges? PB – I’m not sure - I noticed that things take a long time with toolkit 0.11.X JW – Which OFFTK versionare you using CC? CC – 0.10.6 JW – Ok, I think FB CAN work with new toolkit, but it may break caching logic, so that could take a long time.
JW – Some fixes for fragmenter and OFFTK following toolkit 0.11.1 release (all just broken tests) DN – Should we advertise 0.11.0 on linkedin? JW – I thought we did? If we didn’t advertise 0.11.0 on linkedin, we totally should! DN – We didn’t JW – Let’s talk at lead team meeting - We can probably reuse the slack postings or ad board emails.
Starting work again on AM1 proton transfer prevention. May also include canonical atom ordering to stabilize conf gen Helped with workshops Need to push ForceBalance and BespokeFit updates
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