--- 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 AT AT CG CG --- ###
Cite this dataset 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
#### 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_rx1ei5q0x9gy_0 #### Visit the ColabFit Exchange to search additional datasets by author, description, element content and more. https://materials.colabfit.org
# 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
# 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).
#### 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)