Enhancing non-local interaction modeling for ab initio biomolecular calculations and simulations with ViSNet-PIMA

Abstract

AI-based molecular dynamics simulation brings ab initio calculations to biomolecules in an efficient way, in which the machine learning force field (MLFF) locates at the central position by accurately predicting the molecular energies and forces. Most existing MLFFs assume localized interatomic interactions, limiting their ability to accurately model non-local interactions, which are crucial in biomolecular dynamics. In this study, we introduce ViSNet-PIMA, which efficiently learns non-local interactions by physics-informed multipole aggregator (PIMA) and accurately encodes molecular geometric information. ViSNet-PIMA outperforms all state-of-the-art MLFFs for energy and force predictions of different kinds of biomolecules and various conformations on MD22 and AIMD-Chig datasets, while adapting the PIMA blocks into other MLFFs further achieves 55.1% performance gains, demonstrating the superiority of ViSNet-PIMA and the universality of the model design. Furthermore, we propose AI2BMD-PIMA to incorporate ViSNet-PIMA into AI2BMD simulation program by introducing "Transfer Learning-Pretraining-Finetuning" scheme and replacing molecular mechanics-based non-local calculations among protein fragments with ViSNet-PIMA, which reduces AI2BMDs energy and force calculation errors by more than 50% for different protein conformations and protein folding and unfolding processes. ViSNet-PIMA advances ab initio calculation for the entire biomolecules, amplifying the application values of AI-based molecular dynamics simulations and property calculations in biochemical research.