articleThe Journal of Physical Chemistry BDec 28, 2023GREEN OA

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

PEPeter EastmanRGRaimondas GalvelisRPRaúl P. PeláezCRCharlles R. A. AbreuSEStephen E. Farr

Stanford University · Universitat Pompeu Fabra · +21 more institutions

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Abstract

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these…

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Topics & keywords

Topics
Keywords
  • Computer science
  • Molecular dynamics
  • CUDA
  • Interface (matter)
  • Artificial intelligence
  • Computational science
  • Machine learning
  • Parallel computing
UN Sustainable Development Goals
  • Affordable and clean energy
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