Chig-AIMD -- ColabFit
Collection
Datasets from Chignolin-Ab Initio Molecular Dynamics in ColabFit format • 6 items • Updated
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property_id string | property_hash string | last_modified timestamp[us] | dataset_id string | multiplicity int32 | software string | method string | energy float64 | atomic_forces list | cauchy_stress list | cauchy_stress_volume_normalized bool | electronic_band_gap float64 | electronic_band_gap_type string | formation_energy float64 | adsorption_energy float64 | atomization_energy float64 | max_force_norm float64 | mean_force_norm float64 | energy_above_hull float64 | configuration_id string | configuration_hash string | structure_hash string | cell list | positions list | pbc list | chemical_formula_hill string | chemical_formula_reduced string | chemical_formula_anonymous string | elements list | elements_ratios list | atomic_numbers list | nsites int32 | nelements int32 | nperiodic_dimensions int32 | dimension_types list | names list | labels list | property_metadata_path string | configuration_metadata_path string | hash string | configuration_metadata string | property_metadata string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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End of preview.
Cite this dataset
Wang, T., He, X., Li, M., Shao, B., and Liu, T. Chig-AIMD scaffold train. ColabFit, 2023. https://doi.org/10.60732/facc4255
Cite this dataset
Wang, T., He, X., Li, M., Shao, B., and Liu, T. Chig-AIMD scaffold train. ColabFit, 2023. https://doi.org/10.60732/facc4255This dataset has been curated and formatted for the ColabFit Exchange
This dataset is also available on the ColabFit Exchange:
https://materials.colabfit.org/id/DS_7puixss6qd61_0
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Dataset Name
Chig-AIMD scaffold train
Description
Training configurations from the 'scaffold' split of Chig-AIMD. This dataset covers the conformational space of chignolin with DFT-level precision. We sequentially applied replica exchange molecular dynamics (REMD), conventional MD, and ab initio MD (AIMD) simulations on a 10 amino acid protein, Chignolin, and finally collected 2 million biomolecule structures with quantum level energy and force records.
Dataset authors
Tong Wang, Xinheng He, Mingyu Li, Bin Shao, Tie-Yan Liu
Publication
https://doi.org/10.6084/m9.figshare.22786730.v4
Original data link
https://doi.org/10.1038/s41597-023-02465-9
License
CC-BY-4.0
Number of unique molecular configurations
1592662
Number of atoms
264381892
Elements included
C, H, N, O
Properties included
energy, atomic forces
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. Ifcs/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).
ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:
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