Updates | SB Lots of science work. Thinking about WBO fitting. Considering whether it’s ready for sage/whether Sage should be delayed SB – Main issue we imagine is happening with AmberTools is conformer collapse – If positive and negative groups are nearby in a conformer, then we could get large conf charge/proton transfer. Also, if we have closely-spaced conformers, we could get conformers minimizing the same minimum. JW – Possible ways forward could be to JW – Should we aim to get distinct conformers in ELF10? It seems like the current scheme could end up giving us a bunch of very similar conformers
Put together a package for interactive plotting of fitting/mol structure visualization. Used plotly. Working on evaluator issues – Getting nan in gradient calcs, some DASK based issues. JW – I’ll look into doing AmberTools restraints, and ask someone like Jessica to regenerate plot with those, to see if its a night-and-day difference.
MT Continued working on getting exporters to match energies. Currently iterating on a process of 1) get molecule 2) parameterize to System 3) export to other format (OpenMM/GMX). OMM has been easy, Gromacs is hard. Currently working on cyclohexane+ethanol exports. This is matching on 1e-6 for valence terms (for all engines!), and several orders of magnitude higher for nonbonded. Some issues with GMX coordinates only being to 3 digits past the decimal. So, to compare, I have to round off at the same place in OpenMM Currently haven’t checked Constraints Impropers Nonperiodic torsions
DD – Constraints in GMX should be possible – Can make a separate constraints file that gets fed in. It may involve defining groups of atoms and enabling constraints on them by referencing those groups. MT – Currently planning to explicitly not support this now, and warn user that constraints aren’t being written out, and produce the constraint file later down on the roadmap. System object currently handles constraints like the toolkit, where they’re done through a separate handler.
MT – Also thinking about pathway to having a curated set of systems/energy tests for different FFs/chemistries. JW – This was a big point of discussion at a previous interoperability meeting. It may be good to connect up with Chodera about this – We may be able to get a reference set of molecules+energies that we can validate against. MT – I expect that there may be friction where we realize that many things that people are doing with typing/parameterization are actually wrong/underdefined. JW – Could compile our own set of SMIRNOFF and GMX reference energies, and let GMX developers correct us if we’re wrong.
MT – Swails is getting involved in System work, not clear in what capacity. MT – I need to avoid scope creep on the fitting side – While we might eventually replace forcebalance, I don’t consider the replacement as a part of the System objectives. So I’ll make API points that a ML process would need to get the data that it wants, but I won’t implement the ML stuff under the hood.
DD – QCA: Added new submissions from users. Compute is saturated. Currently focused on QCA submission infrastructure improvements. Looking to automate tasks and cache conda data. Next, Partner benchmarks: 7/10 partners are either preparing or running production datasets. Working towards bugfix release of benchmark package – Will include mirror image deduplication. D Hahn is working on OLPS3e energy computations. I’ll be code reviewer for that, and Swope will be scientific/user side reviewer.
Preparing partner datasets for submission. Would like these to be running by early March.
JW PR reviews Onboarding Josh Mitchell (documentation writer) Worked with Slochower on toolkit usage and putting together workflows. Andrew Dalke – Cheminformatics and python wizard, we may bring him on as a contractor Ivan Pulido – Will be a software scientist in Chodera lab soon, bringing him on to OpenFF for a few months.
PB – Lots of WBO work, different potential fits. Studying whether fits/initial proof of concept work can extend to non-congeneric datasets of larger molecules Studying how to use TG’s fingerprinting method to cluster molecules similar to DBSCAN. PEPCONF debugging – My current recommendation is to use second-order methods when we get SCF convergence failures. Seems like Swope is encountering the same problems.
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