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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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Workflow Component : Validation and parameter-labeling of molecules #10

Closed dotsdl closed 3 years ago

dotsdl commented 3 years ago

Parameterization of molecules will be performed with e.g.: 

from openforcefield.typing.engines.smirnoff import ForceField

# Load the OpenFF "Parsley" force field
forcefield = ForceField('openff-1.0.0.offxml')

# Parametrize the topology and return parameters used
off_topology = molecule.to_topology()
molecule_labels = forcefield.label_molecules(off_topology)

The labels can then be fed directly to the Forcefield coverage report #11 generator. An entry-point wrapping this and the coverage report can be placed in openff.benchmark.parameterization.

This step should be performed with each forcefield we are benchmarking.

Molecules that fail this step should be noted and left out of the energy minimization submission. We still want these in the coverage report that consumes the output of this step.

jthorton commented 3 years ago

QCSubmit dataset coverage reporter

jthorton commented 3 years ago

Some molecules that have issues in the archive currently https://github.com/openforcefield/openff-benchmark/issues/5 note that some of the issues are with the BCCs so you may also need to try and generate charges for each molecule to uncover all issues?

dotsdl commented 3 years ago

@j-wags please close if you consider this feature complete.