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Discussion topics
Recording: https://us06web.zoom.us/rec/share/p9d9s_dzVcbFtxUFvgVUfJg7VIJI9S_dvJy7WZ0VCV7rFa6965HaLrqDvF97md89.wy3pk4OKEnY6f13i
Passcode: D*p=3Pcn
Item | Presenter | Notes |
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NAGL2 charge method | LM | DM/BS: have you reported this to Psi4? What have they said? DC: Some QM people I talked to weren’t very surprised that diffuse + PCM didn’t work. CB: If 60% molecules converge, is that all the chemical environments you want to characterise, or are there entire chemical spaces that fall into the 40% failures? CB: do I understand correctly that the MBIS charges are related to the issues? BS: CB, the danger might be that there’s a bug in the code that affects everything and just doesn’t manifest on 60% of them, or there’s an issue with the methodology. I’d be skeptical of this method CB: if you ditch diffuse functions, the wavefunctions you end up with won’t move as much charge onto the relevantly charged atoms with high charge density CB: back in the day I would make locally dense basis sets with diffuse functions on the atoms bearing charge density. This probably won’t save this problem. CB: suggests a delta-ML model that trains to the 60% data with diffuse functions
DM: Next steps? BS: suggests switching up radii and cavity sizes TG: do you opt geometries prior? I used to do a multi-step approach with an easy basis set and increasing the method later (e.g. HF → add diffuse → add PCM). That usually helps with initial guess AMI: I tried reading in vacuum initial guess and that didn’t help. It’s also not supported by QCA. AMI: geometries are optimized in vacuum with B3LYP. Issue is not with geometries, but with SCF convergence of the optimized structure.
DC: if you’re not using a charge scheme, how are you getting around buried atoms in the molecules when you fit to ESP? AMI: thinking of a RESP-like restraint. One concern was that if we just train on ESPs, we may just get RESP charges out BS: is there a problem converging the wavefunction with PCM? AMI: yes. Not specific to MBIS
CB: going back to larger radii on negative atoms, AMI, you said that worked but seemed dodgy. Could we use some of the converged calculations to check if there are artifacts? Would that be a general solution? AMI: do you mean to compare results between calculations? CB: yep. sounds like this could be a path forward AMI: I can compare this. It did work for a couple test cases. You can use UFF and Bondi radii for PCM. Typically UFF is 1.1x, Bondi 1.2x scaled. I scaled UFF to 1.2x in my attempts, which I’ve seen in other codes like Gaussian, so not crazy. BS: Speaking to artifacts DC mentioned, we saw the dipole moment was very sensitive to the radii. CB: Bondii radii are pretty old. There’s other radii sets we could use. Not sure we have a gold standard. Can you read in your own vdW radii? Bondii not necessarily constructed for dipoles/ESPs.
AMI: happy to try vdW scaling quickly. Looking for custom vdW sets could be tricky. DM: does having diffuse functions with different radii always improve results over not having diffuse functions? AMI: I’m not an expert in PCM so I can’t necessarily speak to that. RESP2 averages PCM and vacuum. Vacuum will be quite substantially improved for anions. CB: solvation response will be less pronounced. (see recording ~36 min…) DM: ok, so not an easy answer, a research problem. DM: is there a simple test we could run to check if this improves results?
DC: seeing differences around 0.1e with higher level charge model vs AM1-BCC. Might be able to drop diffuse functions without much effect. AMI: I’ve only looked at neutral molecules so far. Can look at anions too. It might be that the errors introduced by ML and FFs might outweigh everything. AMI: will choose example anion molecule and compare differences. DC: would decide beforehand what change in charge I’d worry about.
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NAGL Zinc charges | | |
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