Individual updates | DN Email from Katharina, feedback on annual report. She’s happy with the annual report, but had some feedback on the claim that governing board asked for biopolymer FF, so she may want a revised version put out. Will discuss with JW later today. MT and CC were on the FF release call when we were kind of invited to participate on the science roadmap building with PIs. Discussion about whether it would be best to have two different roadmaps that would eb aware of each other. JChodera suggested running micro-workshops where ad board members give short updates on their biggest failures and biggest wants. So I invited the ad board to participate and give feedback - KMeier is positive on this. We’ll invite the entire team to these meetings (will be in the ad board time slot). JW – I really like this idea. DN – Yeah, this is a logical followup from the ad board not insisting on a Sage 2.1.0 release.
MT – Re: roadmaps - There seems to be two axes - (academic <--> industry) and (science <--> infrastructure) - I’m not sure which roadmaps are being proposed, but I’d be cautious about assuming significant overlap. So this seems like a tricky area to plan around. DN – A lot of what was discussed was “long term science”, which seems pretty academic. But the short term science seems like it’s of great interest to the industry-supported/consortium roadmap. JW – I’d like the idea of consortium and initiative (academic and industry) roadmaps. But I’m happy to merge infrastructure and science on both sides DD – It seems like it may be ideal to have a single roadmap, with things labeled as “consortium” vs. “initiative”. JW – I’d like us to at least start with separate roadmaps, but we can regularly meet to discuss helping on specific items and making hard commitments to complete tasks/deliverables. DN – This kinda arises from a need to show that NIH money isn’t going to non-NIH goals, and likewise for industry support. DD – I think this could be accomplished by having a column indicating which items are in consortium vs. initiative. DN – I don’t think the initiative roadmap would be too complicated - I think it will be a few items that are longer-term. But the PIs will need to handle the initial prioritization of their tasks before we discuss shared goals.
MT Flurry of smaller patches into Interchange Iterating with JMitchell and JWagner. Working on toolkit around virtual sites. OFF toolkit TIP5P is slightly different from OpenMM TIP5P, we did the math by hand and OFF toolkit positions are correct, OpenMM positions are different. Took a long time so we didn’t look further. Documenting release.
DD PB Spent sometime looking at the phase angles of torsion parameters that have 90/270, which are odd since phase angles are usually 0/180, and there seems to be no need for them. Chris Bayly didn't put them in but Daniel McKay might have some insights about their origin. Was looking at the torsion multiplicity fitting, didn't succeed in the first attempt, some angles (a11, a14) optimized to weird values. Wrapping up incomplete sections in Sage manuscript. Global benchmarking metrics might be deceiving, especially RMSD metric, and there is a need to look at bad chemistries in a tiered approach, with the angles and bonds coming first and then torsions. Found instances of bad phosphorous angles in some of my experimental fits, and the sulfonamide issue with Sage.
CC JW – Getting examples tests running Finished icode handling Worked with MThompson on vsite verification Worked with JMitchell on toolkit showcase refactor, migration guide/changelog finalization, and performance improvements Doing final checks on examples.
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