Updates | MT VSites Gradually adding in functionality, yet to add an “everything bagel” molecule ChargeIncrements are a bit complicated, since they seem to have different meanings in CIMH and VSiteHandler CIMH just adds the increment to each tagged atom VSiteHandler takes some positive/negative charge from the atoms, and put them onto a non-atom
Worked with TG on how our vsites interact with meaning of FD/2FD/3FD – These largely differ by how they define distance (either explicitly, or relative to some other measurement). I’d picked the wrong one initially, but now I’m on the right track. Found a handful of bugs with AMBER energies. Not sure whether these are in the file outputs themselves, or sander settings.
Two toolkit bugs One was a simulation crash bug, was due to using different HMR settings OFFTK #1019 highlighted an error in ParmEd use, which garbled 1-4 energies.
PB Worked on theory benchmark, dataset submission and analysis scripts Tried to reproduce TF’s problem, no success. Re: Chapin meeting – Will we need to do 2d torsiondrives? JW – I’d expect that we might need to do this eventually, but it would be reasonable to restrict to 1D initially, so we can do a cheap first iteration before we commit a lot of resources SB – We have some 2D torsiondrives going, but they’re proper+improper. They’re also taking a really long time, seems like a lot of dead jobs. Not sure what’s happening here, may be worth investigating. JW – Could look at the root cause for these – If it’s job pre-emption on the compute clusters, we might consider just spending money on dedicated compute.
JW Vacation for a lot of past two weeks ParmEd/OFFTK #1019 Benchmarking release w/ Dotson. Next up Finish debugging OFFTK #1019 and update notebook Announce new FFs (1.3.1 and 2.0.0-rc1) Followup workshops announcement Fox analysis debugging Benchmarking release 0.10.0 OFFTK release 2021 Roadmap update
SB – How do pharma partners feel about docker?
LW Was off most of the last few days Read CC’s plan for protein FF. Tried making a “null” FF, where I make a protein FF using the amino acid building blocks. Tried using Psiresp to generate charges. OpenEye wrote back to David about atom-order-dependent geometries (and therefore partial charges). They told us to do our own minimization, and when I tried this out (using RDKit to minimize) I got much better charge consistency for different atom orders. SB – Have you tried completely disabling AM1 geometry optimization? LW – Yes, this gives consistent charges. JW – Connor Davel (Boulder undergrad) has shown preliminary data that shows that charges don’t really change if we don’t allow geometry minimization at all SB – It’d be good to check in with CBy to see if there are edge cases where minimization is really important. LW – What kinds of molecules is CD working with? SB – Has anyone tried using PySCF? They seem to have an AM1 implementation
SB – Out on vacation last week Opened PR to QCEngine to do torsiondrives. MolSSI/Dotson will need to review/decide on whether this fits with their architecture qcsubmit is on conda-forge! Now compatible with new namespaces. (fragmenter also got added around the same time) Working on getting bespokefit ready for september workshop – Additional pedantic-friendliness, using fastapi, more microservice-focused architecture.
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