modelforge curated dataset: OpenFF PhAlkEthOH Dataset

Curated OpenFF PhAlkEthOH Dataset:

Minimized full dataset, version "full_dataset_min_v1":

This provides a curated hdf5 file for a subset of the OpenFF PhAlkEthOH dataset designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 12271 total conformers for 12271 unique molecules; only the final energy minimized configuration is included per molecule. This excludes any configurations where the magnitude of the forces on the atoms are greater than 1 hartree/bohr.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module

This curated dataset was generated using the modelforge software at commit :

Link to the source code at this commit:  

Link to the script file used to generate the dataset:

Source Dataset:

PhAlkEthOH: Phenyls, Alkanes, Ethers, and alcohols (OH) 

The PhAlkEthOH dataset contains a collection of optimized geometries of linear and cyclic molecules containing phyl rings, small alkanes, ethers, and alcohols  containing  only elements carbon, oxygen and hydrogen.  For each unique molecule, conformers correspond to snapshots from the optimization trajectory.  All QM datapoints retrieved from The MolSSI qcarchive and were generated using B3LYP-D3BJ/DZVP level of theory, the default theory used for force field development by the Open Force Field Initiative.

Citations:

Related manuscripts:

Bannan CC, Mobley D. ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns. ChemRxiv. 2019; doi:10.26434/chemrxiv.8304578.v1

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:10.1039/d2sc02739a

Source dataset:

Gokey, T,., "OpenFF Sandbox CHO PhAlkEthOH v1.0", 2020, https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-09-18-OpenFF-Sandbox-CHO-PhAlkEthOH