colabfit/MD22_AT_AT_CG_CG

<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 AT AT CG CG. ColabFit, 2023. https://doi.org/10.60732/a87c6d4c</details>

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Dataset Name

MD22 AT AT CG CG

Description

Dataset containing MD trajectories of AT-AT-CG-CG DNA base pairs 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

10153

Number of atoms

1198054

Elements included

C, H, N, O

Properties included

energy, atomic forces <br> <hr>

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
• —Dataset info schema
• —Configuration schema
• —Configuration set schema
• —Configuration set to configuration mapping schema