openmm
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List of infrastructure tasks for 2022. Each task should be linked to its Confluence or GitHub page with more information. See also Science Roadmap 2021 . |
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Infrastructure tasks | Priority | Effort | Blocking science? | Infrastructure Dependencies | Start date | End/Due date | Status | Driver | ||||||||||||||||||
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Architecture / General infrastructure | ||||||||||||||||||||||||||
95%+ core package uptime and deployment (OpenFF TK, s99F, OpenFFs) |
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Add |
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Refresh , consolidate, and prune OpenFF toolkit examples |
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SQM AM1 optimization connectivity change handling |
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Streamline |
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Refactor | Unresolved – Don’t know timeline for adoption – Bring up in leadership/gov board meeting. Infra team will look into completeness of tests/reference values to estimate refactor cost | |||||||||||||||||||||||||
Accept, reject, or request specific feedback for SMIRNOFF spec proposals within 4 weeks of submission |
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Automated upstream RC tests |
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“Did I break something else?” tests against |
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QCA Standards v3 implementation |
| new qca hire? | ||||||||||||||||||||||||
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QCA 2D torsiondrive support (may just need to verify that this works) |
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| Interoperable molecule class | |||||||||||||||||||||||||
Bayesian infrastructure: ML frameworks | Bayesian Fitting | Analytically Differentiable System Object |
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Off-site charges (support for conversion to other packages) |
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| June 2021 |
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Define and maintain specific goals for Bespokefit deployability/stability (succeeds on 95% of minidrugbank? In under some set number CPU-hours? Regression test suite incorporated into CI) |
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Local torsiondrive executor (default qc, ANI, and XTB - a more formalized version of this command line command in |
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Interchange: Have ForceField.create_openmm_system either be deprecated or wrap Interchange call |
| GBSA suport in Interchange Plugin support in Interchange, and a few months of lead time for scientists who need to port parameterhandler plugins | ||||||||||||||||||||||||
Interchange: System combination |
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Interchange: AMBER export |
| Biopolymer topologies SMIRNOFF updates |
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Interchange: GROMACS export |
| Biopolymer topologies SMIRNOFF updates |
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Interchange: OpenMM export |
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Intercharge: LAMMPS export |
| SMIRNOFF updates | ||||||||||||||||||||||||
Interchange: ParmEd export |
| Biopolymer topologies SMIRNOFF updates |
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Interchange: AMBER import |
| Biopolymer topologies |
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Interchange: GROMACS import |
| Biopolymer topologies |
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Interchange: OpenMM import |
| Biopolymer topologies |
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Interchange: ParmEd import |
| Biopolymer topologies |
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Interchange: Track parameter provenance on import (ie, hold a single value for shared GAFF parameters) |
| Biopolymer topologies | ||||||||||||||||||||||||
Interchange: Interfacing with ML-based fitting | Blocked by lack of specification / needs to be broken into more discrete deliverables |
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Interchange: “Book” documentation/user’s guide |
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| June 2020 |
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Remove |
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Toolkit | ||||||||||||||||||||||||||
| Biopolymer fitting | March 2020 |
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Polarizability ParameterHandler |
| Polarizable fitting | ||||||||||||||||||||||||
(Follow up with Jeffry Setiadi Michael Gilson to understand long term plans and infrastructure needs) |
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WBOs for improper torsions | Waiting on research results to assign priority | |||||||||||||||||||||||||
A deep dive into toolkit parametrization differences (Josh Fass SMIRKS differences) / Automate complaining about cases where incoming molecule/chemistry is bad/misformatted |
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Refactor/make our own Exception hierarchy, implement some problems as catch-able warnings. |
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Implement friendly default behavior when loading large molecule datasets/high-volume pipelines, with option for custom validation logic. Consider making moleculefixer for common data problems. |
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openforcefield-core/pydantic refactor (possibly driving a SMIRNOFF spec update) |
| Aromaticity refactor Stereochemistry refactor | ||||||||||||||||||||||||
Remove OpenFF-Toolkit’s hard dependency on OpenMM (migrate to pint/openff-units) (patch) |
| Sep 2021 | 0.11.0 release |
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| RDKit doesn’t have helpful protonation state enumeration; need to publicize and see if community wants to contribute there https://github.com/openforcefield/openforcefield/issues/526 Could use EPIK from schrodinger suite? Example in OpenMolTools | Mar 2020 | July 2020 (incomplete) |
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Interoperable molecule/stereochemistry/aromaticity refactor |
| Need to decide on desired behavior for how stereochemistry and aromaticity is handled. Also need to decide on which molecule formats should be losslessly round-trippable. | ||||||||||||||||||||||||
Biopolymer infrastructure (SMARTS typing optimization) |
| Biopolymer fitting | Dec 31 2020 |
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Biopolymer infrastructure (infra improvement/Topology refactor/automated polymer unit recognition) |
| Biopolymer fitting | Should discuss design with OpenEye |
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Biopolymer infrastructure (graph charges and/or other scalable solution) |
| Biopolymer charge fitting | ||||||||||||||||||||||||
CMAP torsions in OFFTK/SMIRNOFF spec |
| CMAP fitting | ||||||||||||||||||||||||
Fitting | ||||||||||||||||||||||||||
Migrate FF optimization to ML framework |
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QM-MM / iPolQ solvent calcs on QCA |
Needs research cycle: Could another QC program offer performant continuum solvent model and be compatible with QCF? | (Maybe: Way to generate solvent configuration in QCA? Or is this cheap enough to do outside QCA?) | Chapin Cavender Maybe @new-qca-hire Trevor Gokey Jeffrey Wagner | |||||||||||||||||||||||
Single-point QM-MM of a subset of packed/folded protein on QCA |
| Need to decide on a QC program and ensure feature support/QCA compatibility) | ||||||||||||||||||||||||
Benchmarking | ||||||||||||||||||||||||||
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| Mid 2019? |
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Protein Xtal/NMR observable based benchmarking and fitting (chemical shift/scalar couplings/RDCs/kirkwood-buff integrals/etc) (specific effort to be directed by Chapin Cavender) |
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PL Benchmarking on Folding@Home (aligning with architecture from |
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Automated benchmarking + dashboard May include geometry tools (MM minimization, conformer generation, torsion scanning, conformer scoring) |
| (Optional) Reliable QCMol → OFFMol conversion/CMILES deviation checks | ??? |
| Dashboard: Jaime Rodríguez-Guerra (Deactivated) David Dotson John Chodera Trevor Gokey | |||||||||||||||||||||
Documentation / Community / Training | ||||||||||||||||||||||||||
Reference energies data package (curation write-up) |
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| SMIRNOFF updates | Sep 2021 |
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CHARMM-GUI integration / validation |
| A way to create CHARMM residue template files (ParmEd Issue #1103) |
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