Chig-AIMD -- ColabFit
Collection
Datasets from Chignolin-Ab Initio Molecular Dynamics in ColabFit format
•
6 items
•
Updated
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PO_1001604003792431644149703
|
1001604003792431644149703742557879244815669241342645604633568520368230830672676396093079486187868890288673879899988876309267376059325220097267734680061808
| 2025-04-16T18:29:13
|
DS_mzz13lim5qfi_0
| 1
|
ORCA 4.2.1
|
DFT-M06-2X
| -122,767.52213
|
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] |
[] | null | null | null | null | null | null | 5.048671
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] | null |
data/MD/0801/MD_9436855571093698995590801.json
| null | null | null |
{"basis-set": "6-31G*", "hash": "9436855571093698995590801379497766820894303485636277187386990105620045765354417437700198739780875030510837747395743910271166224324612855568560640424154293", "id": "MD_9436855571093698995590801"}
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PO_1001606471132299463306268
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| 2025-04-16T17:03:14
|
DS_mzz13lim5qfi_0
| 1
|
ORCA 4.2.1
|
DFT-M06-2X
| -122,767.393619
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| 2025-04-16T21:30:02
|
DS_mzz13lim5qfi_0
| 1
|
ORCA 4.2.1
|
DFT-M06-2X
| -122,766.304299
|
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End of preview. Expand
in Data Studio
Cite this dataset
Wang, T., He, X., Li, M., Shao, B., and Liu, T. Chig-AIMD scaffold val. ColabFit, 2023. https://doi.org/10.60732/c182723b
Cite this dataset
Wang, T., He, X., Li, M., Shao, B., and Liu, T. Chig-AIMD scaffold val. ColabFit, 2023. https://doi.org/10.60732/c182723bThis 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_mzz13lim5qfi_0
Visit the ColabFit Exchange to search additional datasets by author, description, element content and more.
https://materials.colabfit.org
Dataset Name
Chig-AIMD scaffold val
Description
Validation 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
198978
Number of atoms
33030348
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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