Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications
We previously introduced a "range corrected" Δ-machine learning potential (ΔMLP) that used deep neural networks to improve the accuracy of combined quantum mechanical/molecular mechanical (QM/MM) simulations by correcting both the internal QM and QM/MM interaction energies and forces [J. Chem. Theory Comput. 2021, 17, 6993-7009]. The present work extends this approach to include graph neural networks. Specifically, the approach is applied to the MACE message passing neural network architecture, and a series of AM1/d + MACE models are trained to reproduce PBE0/6-31G* QM/MM energies and forces of model phosphoryl transesterification reactions. Several models are designed to test the transferability of AM1/d + MACE by varying the amount of training data and calculating free energy surfaces of reactions that were not included in the parameter refinement. The transferability is compared to AM1/d + DP models that use the DeepPot-SE (DP) deep neural network architecture. The AM1/d + MACE models are found to reproduce the target free energy surfaces even in instances where the AM1/d + DP models exhibit inaccuracies. We train "end-state" models that include data only from the reactant and product states of the 6 reactions. Unlike the uncorrected AM1/d profiles, the AM1/d + MACE method correctly reproduces a stable pentacoordinated phosphorus intermediate even though the training did not include structures with a similar bonding pattern. Furthermore, the message passing mechanism hyperparameters defining the MACE network are varied to explore their effect on the model's accuracy and performance. The AM1/d + MACE simulations are 28% slower than AM1/d QM/MM when the ΔMLP correction is performed on a graphics processing unit. Our results suggest that the MACE architecture may lead to ΔMLP models with improved transferability.
Authors
- Timothy J. Giese (ORCID: https://orcid.org/0000-0002-0653-9168)
- Jinzhe Zeng (ORCID: https://orcid.org/0000-0002-1515-8172)
- Darrin M. York (ORCID: https://orcid.org/0000-0002-9193-7055)
Institutions
- University of Science and Technology of China (CN)
- Suzhou University of Science and Technology (CN)
- Rutgers Sexual and Reproductive Health and Rights (NL)
- Quantitative BioSciences (US)
Publication Details
- Journal
- The Journal of Physical Chemistry B
- Published
- 2025-05-26
- DOI
- https://doi.org/10.1021/acs.jpcb.5c02006
- Citations
- 8
- Primary Topic
- Machine Learning in Materials Science
- Type
- article
- Field-Weighted Citation Impact
- 4.14
Funders
- National Science Foundation
- National Institutes of Health