Datasets:

colabfit
/

flexible_molecules_JCP2021

configs:
  - config_name: default
    data_files: co/*.parquet
  - config_name: info
    data_files: ds.parquet
  - config_name: configuration_sets
    data_files: cs/*.parquet
  - config_name: config_set_mapping
    data_files: cs_co_map/*.parquet
license: cc0-1.0
tags:
  - molecular dynamics
  - mlip
  - interatomic potential
pretty_name: flexible molecules JCP2021

Cite this dataset
Vassilev-Galindo, V., Fonseca, G., Poltavsky, I., and Tkatchenko, A. flexible molecules JCP2021. ColabFit, 2023. https://doi.org/10.60732/71f8031b

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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. 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).

Cite this dataset Vassilev-Galindo, V., Fonseca, G., Poltavsky, I., and Tkatchenko, A. flexible molecules JCP2021. ColabFit, 2023. https://doi.org/10.60732/71f8031b