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End of preview. Expand in Data Studio
Cite this dataset
Vassilev-Galindo, V., Fonseca, G., Poltavsky, I., and Tkatchenko, A. flexible molecules JCP2021. ColabFit, 2023. https://doi.org/10.60732/71f8031b
Cite this dataset
Vassilev-Galindo, V., Fonseca, G., Poltavsky, I., and Tkatchenko, A. flexible molecules JCP2021. ColabFit, 2023. https://doi.org/10.60732/71f8031bThis 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_i23sbm1o45sj_0
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Dataset Name
flexible molecules JCP2021
Description
Configurations of azobenzene featuring a cis to trans thermal inversion through three channels: inversion, rotation, and rotation assisted by inversion; and configurations of glycine as a simpler comparison molecule. All calculations were performed in FHI-aims software using the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Tkatchenko-Scheffler (TS) method to account for van der Waals (vdW) interactions. The azobenzene sets contain calculations from several different MD simulations, including two long simulations initialized at 300 K; short simulations (300 steps) initialized at 300 K and shorter (.5fs) timestep; four simulations, two starting from each of cis and trans isomer, at 750 K (initialized at 3000 K); and simulations at 50 K (initialized at 300 K). The glycine isomerization set was built using one MD simulation starting from each of two different minima. Initializatin and simulation temperature were 500 K.
Dataset authors
Valentin Vassilev-Galindo, Gregory Fonseca, Igor Poltavsky, Alexandre Tkatchenko
Publication
https://doi.org/10.1063/5.0038516
Original data link
https://doi.org/10.1063/5.0038516
License
CC0-1.0
Number of unique molecular configurations
69174
Number of atoms
1520162
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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