modelforge curated dataset: OpenFF PhAlkEthOH Dataset

<h1><strong>Modelforge Curated OpenFF PhAlkEthOH Dataset:<br>- 1000 configuration test set, final energy minimized configuration only<br>- Version: nc_1000_minimal_v1.1</strong></h1> <p>This provides a curated hdf5 file for a subset of the OpenFF PhAlkEthOH dataset designed to be compatible with&nbsp;<a href="https://github.com/choderalab/modelforge">modelforge</a>, an infrastructure to implement and train NNPs.&nbsp; The This dataset contains 1000 unique records for 1000 total configurations.&nbsp; This contains a single configuration corresponding to the final configuration in the optimization trajectory (i.e., the energy minimized configuration).</p> <p>This excludes any configurations where the magnitude of any forces on the atoms are greater than 1 hartree/bohr.</p> <p>When applicable, the units of properties are provided in the datafile,&nbsp; encoded as strings compatible with the <a href="https://github.com/openforcefield/openff-units/">openff-units</a> package.&nbsp; For more information about the structure of the data file, please see the following:</p> <h2><strong>Source Dataset:</strong></h2> <p>PhAlkEthOH: <strong>Ph</strong>enyls, <strong>Alk</strong>anes, <strong>Eth</strong>ers, and alcohols (<strong>OH</strong>)&nbsp;</p> <p>The PhAlkEthOH dataset contains a collection of optimization trajectories of linear and cyclic molecules containing phyl rings, small alkanes, ethers, and alcohols&nbsp; containing&nbsp; only elements carbon, oxygen and hydrogen.&nbsp; For each unique molecule, configurations correspond to snapshots from the optimization trajectory.&nbsp; All QM datapoints retrieved from <a href="https://qcarchive.molssi.org/">The MolSSI qcarchive</a> and were generated using B3LYP-D3BJ/DZVP level of theory, the default theory used for force field development by the Open Force Field Initiative.</p> <h2><strong>Properties Included:</strong></h2> <ul> <li>atomic_numbers&nbsp;&nbsp;</li> <li>positions &nbsp; &nbsp; &nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"nanometer"</li> </ul> </li> <li>dispersion_correction_gradient&nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dispersion_correction_force &nbsp; &nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dft_total_gradient &nbsp; &nbsp;&nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>dft_total_force&nbsp; <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>total_charge &nbsp;&nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"elementary_charge"</li> </ul> </li> <li>dispersion_correction_energy &nbsp;&nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>dft_total_energy &nbsp; &nbsp; &nbsp;&nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>scf_dipole &nbsp; &nbsp;&nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"elementary_charge * nanometer"</li> </ul> </li> <li>source&nbsp;&nbsp; <ul> <li>"meta_data"</li> </ul> </li> <li>molecular_formula &nbsp; &nbsp; &nbsp;&nbsp; <ul> <li>"meta_data"</li> </ul> </li> <li>canonical_isomeric_explicit_hydrogen_mapped_smiles &nbsp; &nbsp;&nbsp;&nbsp; <ul> <li>"meta_data"</li> </ul> </li> </ul> <h3>Citations:</h3> <p><em>Related manuscripts:</em></p> <ul> <li>Bannan CC, Mobley D. ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns. ChemRxiv. 2019; doi:<a href="https://dx.doi.org/10.26434/chemrxiv.8304578.v1">10.26434/chemrxiv.8304578.v1</a></li> <li>Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Macdonald HE, Takaba K, Chodera JD. End-to-end differentiable construction of molecular mechanics force fields. Chemical Science. 2022;13(41):12016-33. doi:<a href="https://doi.org/10.1039%2Fd2sc02739a" target="_blank" rel="noopener noreferrer">10.1039/d2sc02739a</a></li> </ul> <p><em>Source dataset:</em></p> <ul> <li>Gokey, T,., "OpenFF Sandbox CHO PhAlkEthOH v1.0", 2020, <a href="https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH">https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH</a></li> </ul>