2024-03-18 Meeting notes

 Date

Mar 18, 2024

 Participants

  • @Lily Wang

  • @Marcus Wieder

 Goals

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 Discussion topics

Item

Notes

Item

Notes

Updates on projects

  • publication with Exscientia on FreeSolv HFEs, using different methods (e.g. OpenFF, CGenFF) – basically testing if we can do corrections with NN potentials

    • See systematic distribution in error – have multimodal error distribution

    • Reweighting with ANI potential doesn’t change much

    • Submitted to J Chem Phys

  • modelforge

    • 5 NN potentials implemented, in the process of training them

    • Now at stage where we add docs, tutorials, so people can use it

    • Still doing some re-factoring

    • Close to finishing MVP phase. Not planning to add new NN potentials in near future. Projecting end of April for 1.0 release

  • chiron

    • no updates in past few months

  • deploying trained models? collaboration with Exscientia?

    • still in progress, setting up a marketplace for pre-trained models

    • currently already training NN potentials for this marketplace – setting up reasonable set of hyperparameters to search over. Project that we will have trained models in the next month and the infrastructure to distribute them to people. Outward facing S3 bucket

  • Any further datasets work, e.g. SPICE2, metalloproteins

    • SPICE2

      • PE has finished SPICE2 calculations with SPICE level of theory

      • CI and MW getting OpenFF level of theory working

      • Investigating why SPICE doesn’t work for some people when they want to use it for retraining

      • Working on understanding if there is a problem with the SPICE dataset – still an open scientific question

      • Will focus on this in the next weeks – working towards SPICE3

      • Focusing on the conformations generated and used

        • created with high-temperature MD, which may introduce bias towards MM potential energy surface

    • Metalloproteins

      • Genentech internally accepted project last week, getting funding

      • Starting up now

 

 

 

 

 

 

 Action items

 Decisions