Coarse-grained methanol trajectory
Description
This dataset is a supplement to the paper "Thermodynamic Transferability in Coarse-Grained Force Fields using Graph Neural Networks," available at https://arxiv.org/abs/2406.12112.
To create this dataset, an all-atom trajectory of liquid methanol was generated using the GROMOS 54A7 force field and the LAMMPS software package. The coarse-grained mapping described in the aforementioned paper was applied to the trajectory; the resulting positions, velocities, and forces are provided here. Additionally, the periodic cell is reported, as well as values of the radial distribution function calculated using the coarse-grained positions. For completeness, mass and species arrays are also included.
The original all-atom trajectory was generated using a Nosé-Hoover thermostat at 700 K. After equilibration, 50,000 timesteps of 1 fs were computed and every 500th frame recorded. The resulting 100 frames were used to generate this dataset.
The data is stored in a single Numpy .npz file, which contains eight arrays:
| key | shape | size (bytes) | data units |
| cells | (100, 3, 3) | 7200 | Å |
| forces | (100, 1024, 3) | 2457600 | kcal/mol/Å |
| masses | (100, 1024) | 819200 | amu |
| positions | (100, 1024, 3) | 2457600 | Å |
| rdf_bins | (300,) | 2400 | Å |
| rdf_values | (300,) | 2400 | unitless |
| species | (100, 1024) | 819200 | unitless |
| velocities | (100, 1024, 3) | 2457600 | Å/ps |
Total size of file: 9.03 MB
Files
Files
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Additional details
Related works
- Is supplement to
- Preprint: arXiv:2406.12112 (arXiv)