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openforcefield / openff-benchmark

Comparison benchmarks between public force fields and Open Force Field Initiative force fields
MIT License
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[WIP] Energy minimization compute deployment / execution #17

Closed dotsdl closed 3 years ago

dotsdl commented 3 years ago

Description

This PR addresses #12.

We will want to merge this as soon as we have reached basic functionality (protocol executes on a test molecule). A follow-up PR will focus on error handling and performance.

Todos

Status

dotsdl commented 3 years ago

We now have both submission and export entry-points in place. Need to write up initial QM-then-MM protocol next.

This is ready for an initial review @j-wags when you get the chance. There may be many details I failed to capture.

dotsdl commented 3 years ago

Thanks for the review @jthorton!

@dfhahn, if you like you can give this branch a play using the approach in the demo notebook to generate the inputs needed for downstream analysis. Note that in this notebook we first generate the QM optimizations, then export the final geometries with initial and final energies as key-values in the SDF files. Then, we use those QM SDFs as our inputs for the MM optimizations.

I believe the resulting outputs should be everything you need for downstream analysis. Please let us know if this presents problems, or if you think we could be structuring the compute approach differently to make analysis easier.

dotsdl commented 3 years ago

Merging, as now need to do some synthesis work with the CLI to string together multiple workflow components.