Datasets:
File size: 3,180 Bytes
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configs:
- config_name: default
data_files: "co/*.parquet"
- config_name: info
data_files: "ds.parquet"
license: cc0-1.0
tags:
- molecular dynamics
- mlip
- interatomic potential
pretty_name: MD22 DHA
---
### <details><summary>Cite this dataset </summary>Chmiela, S., Vassilev-Galindo, V., Unke, O. T., Kabylda, A., Sauceda, H. E., Tkatchenko, A., and Müller, K. _MD22 DHA_. ColabFit, 2023. https://doi.org/10.60732/9d9083b8</details>
#### This 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_xwmthngerf71_0
#### Visit the ColabFit Exchange to search additional datasets by author, description, element content and more.
https://materials.colabfit.org
<br><hr>
# Dataset Name
MD22 DHA
### Description
Dataset containing MD trajectories of DHA (docosahexaenoic acid) from the MD22 benchmark set. MD22 represents a collection of datasets in a benchmark that can be considered an updated version of the MD17 benchmark datasets, including more challenges with respect to system size, flexibility and degree of non-locality. The datasets in MD22 include MD trajectories of the protein Ac-Ala3-NHMe; the lipid DHA (docosahexaenoic acid); the carbohydrate stachyose; nucleic acids AT-AT and AT-AT-CG-CG; and the buckyball catcher and double-walled nanotube supramolecules. Each of these is included here in a separate dataset, as represented on sgdml.org. Calculations were performed using FHI-aims and i-Pi software at the DFT-PBE+MBD level of theory. Trajectories were sampled at temperatures between 400-500 K at 1 fs resolution.
### Dataset authors
Stefan Chmiela, Valentin Vassilev-Galindo, Oliver T. Unke, Adil Kabylda, Huziel E. Sauceda, Alexandre Tkatchenko, Klaus-Robert Müller
### Publication
https://doi.org/10.1126/sciadv.adf0873
### Original data link
http://sgdml.org/
### License
CC0-1.0
### Number of unique molecular configurations
69744
### Number of atoms
3905664
### Elements included
C, H, O
### Properties included
energy, atomic forces
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# 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).
<br>
#### ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:
- [Parquet parsing: example code](https://materials.colabfit.org/docs/how_to_use_parquet)
- [Dataset info schema](https://materials.colabfit.org/docs/dataset_schema)
- [Configuration schema](https://materials.colabfit.org/docs/configuration_schema)
- [Configuration set schema](https://materials.colabfit.org/docs/configuration_set_schema)
- [Configuration set to configuration mapping schema](https://materials.colabfit.org/docs/cs_co_mapping_schema)
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