choderalab/geometry-benchmark-espaloma: Small molecule geometry benchmark dataset to validate espaloma-0.3

This is a collection of preprocessed QM and MM optimized structures needed to perform the small molecule geometry benchmark study, described in the espaloma-0.3 paper:

Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara, Mike Henry, Hugo MacDermott Opeskin, John D. Chodera, Yuanqing Wang. "Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond." (TBA)

This benchmark study calculates and compares the RMSD, TFD, and ddE metrics for a specified set of MM force fields. The initial optimized structures were sourced from the OpenFF Industry Benchmark Season 1 v1.1 dataset, which is available through  QCArchive. More details about the preprocessing steps is available at https://github.com/choderalab/geometry-benchmark-espaloma/tree/main/qc-opt-geo.

02-chunks.tar.gz: QM optimized structures chunked into small file sizes.

02-outputs-openff-2.0.0-espaloma-0.3.0rc1.tar.gz: MM optimized structures using openff-2.0.0 and espaloma-0.3.0rc1 force field (former release candidate of espaloma-0.3)

02-outputs-espaloma-0.3.0rc6.tar.gz: MM optimized structures using espaloma-0.3.0rc6 (espaloma-0.3) force field

02-outputs-openff-2.1.0.tar.gz: MM optimized structures using openff-2.1.0 force field