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

<p>This is a collection of preprocessed QM and MM optimized structures needed to perform the small molecule geometry benchmark study, described in the <strong>espaloma-0.3</strong> paper:</p> <p>Kenichiro Takaba, Iv&aacute;n Pulido,&nbsp;Pavan Kumar Behara, Mike Henry, Hugo MacDermott Opeskin, John D. Chodera, Yuanqing Wang.&nbsp;&quot;Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond&quot; (<a href="https://arxiv.org/abs/2307.07085">arXiv:2307.07085</a>)</p> <p>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&nbsp;sourced from the&nbsp;<a href="https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-06-04-OpenFF-Industry-Benchmark-Season-1-v1.1">OpenFF Industry Benchmark Season 1 v1.1</a>&nbsp;dataset, which is available through &nbsp;<a href="https://qcarchive.molssi.org/">QCArchive</a>.&nbsp;More details about the preprocessing steps is available at&nbsp;<a href="https://github.com/choderalab/geometry-benchmark-espaloma/tree/main/qc-opt-geo">https://github.com/choderalab/geometry-benchmark-espaloma/tree/main/qc-opt-geo</a>.</p> <ul> <li><strong>02-chunks.tar.gz</strong>:&nbsp;QM optimized structures chunked into small file sizes.</li> <li><strong>02-outputs-openff-2.0.0-espaloma-0.3.0rc1.tar.gz</strong>:&nbsp;MM optimized structures using openff-2.0.0 and espaloma-0.3.0rc1 force field (former release candidate of espaloma-0.3)</li> <li><strong>02-outputs-gaff2.11.tar.gz</strong>:&nbsp;MM optimized structures using gaff-2.11 force field</li> <li><strong>02-outputs-espaloma-0.3.0rc6.tar.gz</strong>:&nbsp;MM optimized structures using espaloma-0.3.0rc6 (espaloma-0.3) force field</li> <li><strong>02-outputs-openff-2.1.0.tar.gz</strong>: MM optimized structures using openff-2.1.0 force field</li> </ul>