Published February 20, 2024
| Version v1
Journal article
Open
Beyond MD17: The reactive xxMD dataset
Creators
- 1. University of Chicago
- 2. University of Minnesota
Description
System specific neural force fields (NFFs) have gained popularity in computational chemistry. One of the most popular datasets as a bencharmk to develop NFF models is the MD17 dataset and its subsequent extension. These datasets comprise geometries from the equilibrium region of the ground electronic state potential energy surface, sampled from direct adiabatic dynamics. However, many chemical reactions involve significant molecular geometrical deformations, for example, bond breaking. Therefore, MD17 is inadequate to represent a chemical reaction. To address this limitation in MD17, we introduce a new dataset, called Extended Excited-state Molecular Dynamics (xxMD) dataset. The xxMD dataset involves geometries sampled from direct nonadiabatic dynamics, and the energies are computed at both multireference wavefunction theory and density functional theory. We show that the xxMD dataset involves diverse geometries which represent chemical reactions. Assessment of NFF models on xxMD dataset reveals significantly higher predictive errors than those reported for MD17 and its variants. This work underscores the challenges faced in crafting a generalizable NFF model with extrapolation capability.
Data availability
Nonadiabatic dynamics are performed with Surface Hopping with Arbitrart Coupling (SHARC) code, which is available at https://github.com/sharc-md/sharc. SchNet, DimeNet++ and SphereNet are available as implemented in the Dive Into Graphs package (https://github.com/divelab/DIG.git). NequIP package is available at https://github.com/mir-group/nequip.git. Allegro package is available at https://github.com/mir-group/allegro. MACE package is available at https://github.com/ACEsuit/mace.git. All packages are up-to-date at the data of the publication. All the trainings are done with single precision float format. SchNet, DPP and SPN models are initialized using the default hyperparameters shipped with the packages. Allegro hyperameters can be found at https://github.com/mir-group/allegro/blob/main/configs/example.yaml, NequIP hyperparameters are available at https://github.com/mir-group/nequip/blob/main/configs/example.yaml, MACE hyperparameters are available at https://github.com/ACEsuit/mace. Since Dive Into Graphs package doesn't implement the scale and shift of the energy, we manually rescaled the energy by substracting the energy of the configuration with the lowest potential energy.Files
Beyond-MD17.pdf
Files
(5.0 MB)
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Supplementary information md5:a0011c11c91028408d7593c86395b853 |
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Additional details
Identifiers
- DOI
- 10.1038/s41597-024-03019-3
- Other
- oai:uchicago.tind.io:11131
Funding
- AFOSR MURI
- FA9550-21-1-0209