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Jeffrey Wagner

David Dotson

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Discussion topics

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Notes

Planning

  • Goal is to find inputs that make software do something wrong, DON’T try to diagnose, just report on the issue tracker.

Generic workflow

Code Block
conda install -y anaconda-client -n base
conda env create openforcefield/openff-benchmark-optimization
conda activate openff-benchmark-optimization
git clone https://github.com/openforcefield/openff-benchmark.git
cd openff-benchmark
pip install -e .
Code Block
# preprocess
openff-benchmark preprocess validate -g BBB data/*sdf
openff-benchmark preprocess generate-conformers 1-validate_and_assign/
openff-benchmark preprocess coverage-report 2-generate_conformers openff_unconstrained-1.3.0.offxml

# optimize
## qm calculations
openff-benchmark optimize execute --season "1:1" -o 3-export-compute-qm 2-generate_conformers/
## mm calculations
openff-benchmark optimize execute --season "1:2" -o 3-export-compute-mm 3-export-compute-qm/b3lyp-d3bj/dzvp/

analysis 
openff-benchmark report compare-forcefields --input-path 3-export-compute-qm/ --input-path 3-export-compute-mm --ref_method b3lyp-d3bj --output_directory 4-compare_forcefields

plots
openff-benchmark report plots --input-path 4-compare_conformers --ref_method b3lyp-d3bj

Action items

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Decisions