open force field

An open and collaborative approach to better force fields

April 17, 2019 Advisory Board Meeting

Posted on 17 Apr 2019 by Arjun Narayanan and Karmen Čondić-Jurkić

The Open Force Field Consortium Advisory Board met on 17 April 2019. The minutes are summarized as follows:

  • K. Condic-Jurkic to take over future agenda planning with input from D. Kuhn, I. Craig, A. Narayanan
  • Release update by Jeff Wagner:
    • 0.2.1 bugfix release on the 12th after initial 0.2.0 release on 8th
      • Version numbers indicate API is still in flux, there may be function call changes, etc. in later versions, e.g., 0.3, 0.4, …
      • Aiming to have more established base by version 1.0.0
    • Highlighted features of new release:
      • Independent of OpenEye by providing RDKit Cheminformatics support
      • The biggest issues appeared in aromaticity perception, but this has been addressed
      • Likely difference in partial charge assignment due to different methods for producing AM1-BCC charges (OpenEye vs. AmberTools for RDKit)
      • No differences in available functionality
      • Changes to internal data structures to facilitate FF improvement
      • ForceField class is an example, allowing parameter changes with python before assignment
    • Short-term goals
      • Tarball build for non-Conda installation
      • Reading charges from SDF using standardized charge fields
      • Support for library charges for automated assignment
      • Fractional bond order interpolation
      • GBSA parameter assignment
      • Better file format conversion support
    • Toolkit development progress can be tracked on github
    • Video tutorial
    • Initially minor releases may come out weekly (e.g. 0.2.2, 0.2.3) while more significant changes may come out monthly (e.g. 0.3, 0.4)
    • Best places to go with problems (in no particular order):
    • Support for both RDKit and OE toolkits for now, long-term support will depend on the amount of resources available to maintain it
  • Applications/workflows
    • Examples of using SMIRNOFF in different ways would be helpful
    • Robustly developed workflows may be out of scope right now and the primary focus of OpenFF is force field development - making it easy for others to build their own apps using OpenFF resources
    • Example usage can be provided; requests in #documentation channel
  • Hiring Update
    • Still trying to fill position for bespoke torsion fitting
    • Contract extension for Y. Qiu (Wang) and D. Slochower (Gilson) to work on ForceBalance parameter fitting and binding energy benchmarks, respectively
  • Next meeting
    • Scientific updates highlighting scientific progress on the following topics:
    • Where we were when we met in January;
    • What progress has been made;
    • What is happening next?
    • Update on finances
  • Other stuff:
    • OpenFF Seminar Series – contact David with ideas for speakers and topics of interest
    • Contact David/Karmen if you know of any additional interested pharma partners
    • Adding people on Slack
    • Karmen to try to provide digestible summaries of scientific progress in subgroups