2021-04-29 Force Field Release meeting notes
Date
Apr 27, 2021
Participants
@Pavan Behara
@Simon Boothroyd
@David Mobley
@Christopher Bayly
@Simon Boothroyd
@Jessica Maat (Deactivated)
@Owen Madin
@Hyesu Jang
@Joshua Horton
@Trevor Gokey
@Jeffrey Wagner
Goals
Discussion topics
Time | Item | Presenter | Notes |
|---|---|---|---|
| IC Hessian fitting |
| HJ: I can present results in the next meeting, almost wrapping it up. |
| Cutom nonbonded forces/functional form |
| DC: John mentioned some change to the FF format, any updates on that, JW & SB? SB/JW: Cutom nonbonded forces is still work in progress, hopefully by next release. |
| Benchmark infra |
| JW: SB, you asked about the reproducibility of Lim & Hahn results with the new openff-benhcmark infra, I can go through that. SB: Yeah, I am looking more for the fractal instance type of doing it. |
| Sulfonamide |
| CB: Any progress on the sulfonamide pathologies? PB: Not yet, I still have to do some refit with the molecules matching those parameters from Gen 2 sets. CB: The equilibrium angles are converging to 90 in 4-membered ring, 60 in 3-membered ring, etc., so we need to know why it is happening? DLM: It looks like if there is a difference in equilibrium angles then we may have to split the parameter? CB: I am concerned that we will be imparting the same pathologies in Trevor’s work, we don’t need the equilibrium angles to be 90 for these parameters. PB: In FB we’re already tying to reduce the delta between QM and MM geometry CB: Then, I’m wondering what could drive tetrahedral hypervalent sulfur to have these small valence angles SB: Maybe we should do a “canary” test using a sp2 carbon. CB: I think the optimizer will need to kow what a “normal” alkane would look like, so this test case should ahve some inear alkanes as well. SB: Agree. The above test will tell us whether the ring geometries are driving the problem or now. TG: Following yesterday’s discussion, that’s one of the experiments that we talked about – see how ring terms affect linear alkane terms. So we’d compare |
| Openff-benchmark |
| SB – Will current openff-benchmark reproduce Lim+Hahn study? JW – It should come close, but likely not exact JW’s “cheat sheet” for running benchmarking workflow locally/in docker: https://openforcefield.atlassian.net/wiki/spaces/MEET/pages/1108246529 DD’s “general instructions” for external partners: https://openforcefield.atlassian.net/wiki/spaces/PS/pages/971898891/Optimization+Benchmarking+Protocol+-+Season+1#C.-Multi-node%2C-no-server%2Fmanager-setup SB: What’re the validation tests for the infrastructure? JW: Here are some of the tests we did before we put it into the hands of industry people, do you have anything in specific you want to see? SB: Some sanity checks on the numbers we are getting out by manually looking at a smaller set of molecules or even a single molecule and whether we are getting the right units, etc., like regression tests JW: Yeah, I think this is a good idea, will add on issue tracker. SB: Thanks for doing that. JW: Opened |
| Enumerating stereochemistry |
| JW: One thing we learned in discussions with Dalke is not to worry about roundtrips much |
| QM benchmarking |
| PB – When I’m looking at possible methods to include in the benchmark, which programs can I use? Can we get new methods added to psi4? What chemical/computational constraints should I consider?
|
|
|
|
|