Primary Driver | |||||||
Approvers | Jeffrey Wagner John Chodera Richard Gowers Project approvers agreed to dissolve as goals were completed on 2023_10_30 | ||||||
Supporting Drivers | |||||||
Stakeholders | Simon Boothroyd Irfan Alibay Richard Gowers David Swenson Jeffry Setiadi Lorenzo D'Amore Lily Wang Antonia Mey David Mobley | ||||||
Project Manager | |||||||
Decision authority | Unanimity of Primary Driver and two Approvers (absences are vetos), only in synchronous meetings Veto authority: Primary Driver, any Approver | ||||||
Discussion/ Notification Venue | Weekly meetings (decision forum) #free-energy-benchmarking channel on OpenFF slack (notification and discussion, no major decisions allowed here)
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Objective | Leverage Folding@Home for automated, continuous benchmarking of new generations of OpenFF forcefields via binding free energy calculations for a library of protein-ligand systems. | ||||||
Due date |
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Status |
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Problem Statement
Thus far in the project, protein-ligand benchmarks for OpenFF have been a manual process performed on Janssen cluster resources. As new generations of OpenFF forcefields are released, the burden of executing free energy calculations to assess improvement and deficiency will increase, as will the computational cost.
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Leveraging the immense computational resources provided by Folding@Home for near-continuous free energy benchmarking of new force fields against a library of protein-ligand systems.
Introducing automation that minimizes human-in-the-loop requirements for this benchmarking into the future.
Executing free energy calculations via both Gromacs and OpenMM.
Current project specification
(The link below should be considered an authoritative source of truth for this project at the moment. This may be updated in the future)
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Milestones and deadlines
Milestone | Deadline | Status | Completion | ||||||
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Working group recruitment “Read the google doc, provide use cases in the form of “I expect to put X in as an input, and get Y out as an output. State availability for weekly meetings starting as early as Feb 8” | Feb 4 2022 |
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First meeting - How project is managed, open discussion of use cases | Feb 15 2022 |
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Second meeting - Further refinement of use cases | Feb 22 2022 |
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Scope/use case review | Mar 8 2022 |
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Initial API defined (example notebook or command block for each user story?) | 2022.09.15 |
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alchemiscale release 0.1.0 | 2022.09.15 |
| 2023.04.17 | ||||||
protein-ligand-benchmark release 0.3.0 | 2022.09.15 |
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“MVP” - Core infrastructure stand-up as development environment to enable rapid iteration, involvement of stakeholders | 2022.09.15 |
| 2023.04.21 | ||||||
Software development, integration and testing cycles | 2022.09.15 |
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Production environment stand-up and deployment; ideally using promotion mechanism from a QA environment | 2022.10.01 |
| 2023.04.23 |
Reference materials
https://openforcefield.atlassian.net/wiki/spaces/PS/pages/1806761985
Github link macro link https://github.com/choderalab/perses Github link macro link https://github.com/OpenFreeEnergy/gufe Github link macro link https://github.com/openforcefield/protein-ligand-benchmark https://docs.google.com/document/d/1wcTy4TqBIGbxdt9p2reVTY4J5iKAzF673DQsZeZ8vg8/edit?pli=1#
https://drive.google.com/file/d/1_N3yFBRKU8HoE4XCSfPrY26UFlncVGA8/view?pli=1
https://drive.google.com/file/d/1XRpJ9OELd005BCZRn7uwEpMqu70_f8yh/view