Performance benchmarks for OpenFE Protocols
The benchmark simulation scripts are found under benchmark.
md_benchmark.py: this runs conventional MD using OpenMM (uses an underlying OpenFE Protocol for conventional MD).
rbfe_benchmark.py: this runs a hybrid topology RBFE using OpenMMTools + OpenMM with OpenFE.
You can run the scripts in the following manner::
python rbfe_benchmark.py --input_file ../data/benchmark.json --output_file rbfe_benchmark.out
This will output a JSON serialized dictionary keyed by system names and values with the performance in ns/day.
You can see the notebook under results on how to analyze these results.
Everything here is under an MIT license.