Enabling Biomolecular Simulations with Neural Network Potentials in GROMACS

TL;DR

This paper introduces a flexible interface in GROMACS that integrates neural network potentials trained in PyTorch into molecular dynamics simulations, enabling advanced biomolecular modeling and free energy calculations.

Contribution

The authors developed a versatile, architecture-agnostic interface for NNPs in GROMACS, facilitating seamless integration of machine learning potentials into biomolecular MD workflows.

Findings

Successfully integrated NNPs into GROMACS for biomolecular simulations.

Demonstrated enhanced sampling and free energy calculations using the interface.

Benchmarked performance across different NNP architectures in water systems.

Abstract

Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with existing methodologies. To address this, we here present an interface for hybrid machine learning/molecular mechanics (ML/MM) simulations implemented in the widely used MD code GROMACS. The interface enables NNPs trained in the PyTorch framework to contribute energies and forces during MD simulations, either for selected subsets or entire molecular systems. By defining a flexible set of model inputs and outputs, the interface is agnostic to specific NNP architectures and can accommodate a wide range of descriptor-based and message-passing models. In particular, the design integrates NNP inference seamlessly into the extensive GROMACS molecular simulation ecosystem, providing users with the capability to straightforwardly combine NNPs with existing advanced sampling and free energy workflows. We demonstrate the capabilities of the interface using several representative applications, including enhanced sampling of peptide torsional free energy landscapes, absolute solvation free energy calculations, and protein--ligand simulations. We also run performance benchmarks on water boxes for several different NNP architectures. Our interface is available in recent GROMACS releases, and we believe it will provide a practical foundation for incorporating machine learning potentials into production MD simulations of biomolecular systems.