Feb 19, 2020 Advisory Board Meeting
Posted on 19 Feb 2020 by Karmen Condic-Jurkic
The Open Force Field Consortium Advisory Board met on February 19, 2020. The minutes are summarized as follows:
Next force field release plans
- I. Craig (BASF) reported some issues with nitrogen parameters in tetrazoles, and H. Jang has updated a couple of parameters in the recently released minor release -
- D. Mobley presented some benchmarking results from V. Lim’s study of conformer energies and geometries. For geometry comparison, RMSD and torsion fingerprinting deviation (TFD) were used as similarity measures. The aim was to find parameters that may lead to higher geometric deviations in RMSD/TFG.
- C. Bayly and others agreed that this seems like an excellent diagnostic tool for identification of pathological cases, but also potentially for other purposes, creating an example notebook was recommended.
- For the next FF release, the aim is to expand QM datasets, while improving molecule set selection to reduce overrepresentation of certain species.
- J. Chodera announced creation of a benchmarking dashboard, which will be developed in the near future, for exploring OpenFF datasets and comparison of different variables, including conformer energies, geometries, physical properties, and free energy data.
- The question is raised about the best way to demonstrate progress and improvements achieved for the Consortium partners to share with their management. Any feedback is welcome.
- Desired benchmarking results include binding free energies (for protein-ligand and host-guest systems), improved protein-ligand design (for example, ligand conformer scoring – how to find 50 lowest energy conformers out of 1000, comparison with protein-ligand datasets. For the latter, a clear comparison protocol is required.
- X. Hou and A. Gobbi can provide some molecule sets for this purpose.
- Crystal structure comparisons are not of the immediate interest.
NIH grant announcement
- M. Shirts and J. Chodera announced that the Open Force Field Initiative has been awarded the NIH grant to develop biopolymer force fields using Open Force Field framework and build Bayesian inference infrastructure for force field parameterization. This grant will complement the existing efforts focused on small molecule force fields, funded by the Open Force Field Consortium.
- David Cerutti will join as a member of the OpenFF team and lead the biopolymer parameterization efforts, which will start with porting Amber protein force fields to SMIRNOFF format.
- Governing Board members / Ad. Board functions elections coming up. A clear voting protocol to be defined.
- Daniel Kuhn wants to step down as the chair, T. Fox and K. Meier willing to remain in their Gov. Board roles
- Mark Mackey (Cresset) volunteered for the Chair, X. Hou also potentially interested for the role.
- Provisional financial report for Y1 and Y2 provided, the full report is still being processed.
- Registration for the in-person meeting in Boston (May 4-5) is open.
- The OpenFF Initiative has started using Confluence for project management and better documentation of research processes.