Datasets:

colabfit
/

SPICE_2023

configs:
  - config_name: default
    data_files: co/*.parquet
  - config_name: info
    data_files: ds.parquet
  - config_name: configuration_sets
    data_files: cs/*.parquet
  - config_name: config_set_mapping
    data_files: cs_co_map/*.parquet
license: mit
tags:
  - molecular dynamics
  - mlip
  - interatomic potential
pretty_name: SPICE 2023

Cite this dataset
Eastman, P., Behara, P. K., Dotson, D. L., Galvelis, R., Herr, J. E., Horton, J. T., Mao, Y., Chodera, J. D., Pritchard, B. P., Wang, Y., Fabritiis, G. D., and Markland, T. E. SPICE 2023. ColabFit, 2023. https://doi.org/10.60732/a613a175

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This dataset is also available on the ColabFit Exchange:

https://materials.colabfit.org/id/DS_kg0dv12aiq97_0

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Dataset Name

SPICE 2023

Description

SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. Subsets of the dataset include the following: dipeptides: these provide comprehensive sampling of the covalent interactions found in proteins; solvated amino acids: these provide sampling of protein-water and water-water interactions; PubChem molecules: These sample a very wide variety of drug-like small molecules; monomer and dimer structures from DES370K: these provide sampling of a wide variety of non-covalent interactions; ion pairs: these provide further sampling of Coulomb interactions over a range of distances.

Dataset authors

Peter Eastman, Pavan Kumar Behara, David L. Dotson, Raimondas Galvelis, John E. Herr, Josh T. Horton, Yuezhi Mao, John D. Chodera, Benjamin P. Pritchard, Yuanqing Wang, Gianni De Fabritiis, Thomas E. Markland

Publication

https://doi.org/10.1038/s41597-022-01882-6

Original data link

https://doi.org/10.5281/zenodo.8222043

License

MIT

Number of unique molecular configurations

116504

Number of atoms

3382829

Elements included

Br, C, Ca, Cl, F, H, I, K, Li, N, Na, O, P, S

Properties included

energy, formation energy

Usage

ds.parquet : Aggregated dataset information.
co/ directory: Configuration rows each include a structure, calculated properties, and metadata.
cs/ directory : Configuration sets are subsets of configurations grouped by some common characteristic. If cs/ does not exist, no configurations sets have been defined for this dataset.
cs_co_map/ directory : The mapping of configurations to configuration sets (if defined).

Cite this dataset Eastman, P., Behara, P. K., Dotson, D. L., Galvelis, R., Herr, J. E., Horton, J. T., Mao, Y., Chodera, J. D., Pritchard, B. P., Wang, Y., Fabritiis, G. D., and Markland, T. E. SPICE 2023. ColabFit, 2023. https://doi.org/10.60732/a613a175