Dataset Information

TorchMD: A Deep Learning Framework for Molecular Simulations.

ABSTRACT: Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning approaches. Here, we present TorchMD, a framework for molecular simulations with mixed classical and machine learning potentials. All force computations including bond, angle, dihedral, Lennard-Jones, and Coulomb interactions are expressed as PyTorch arrays and operations. Moreover, TorchMD enables learning and simulating neural network potentials. We validate it using standard Amber all-atom simulations, learning an ab initio potential, performing an end-to-end training, and finally learning and simulating a coarse-grained model for protein folding. We believe that TorchMD provides a useful tool set to support molecular simulations of machine learning potentials. Code and data are freely available at github.com/torchmd.

SUBMITTER: Doerr S

PROVIDER: S-EPMC8486166 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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TorchMD: A Deep Learning Framework for Molecular Simulations.

Doerr Stefan S Majewski Maciej M Pérez Adrià A Krämer Andreas A Clementi Cecilia C Noe Frank F Giorgino Toni T De Fabritiis Gianni G

Journal of chemical theory and computation 20210317 4

Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning approaches. Here, we present TorchMD, a framework for molecular simulations with mixed classical and machine learning potentials. All force computations including bond, angle, dihedral, Lennard-Jones, and Coulomb interactions are expressed as PyTorch arrays a ...[more]

PMID: 33729795

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Dataset Information

TorchMD: A Deep Learning Framework for Molecular Simulations.

Publications

TorchMD: A Deep Learning Framework for Molecular Simulations.

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