论文标题

Torchmd:分子模拟的深度学习框架

TorchMD: A deep learning framework for molecular simulations

论文作者

Doerr, Stefan, Majewsk, Maciej, Pérez, Adrià, Krämer, Andreas, Clementi, Cecilia, Noe, Frank, Giorgino, Toni, De Fabritiis, Gianni

论文摘要

分子动力学模拟通过依靠经验潜能提供了分子的机械描述。可以改善使用机器学习方法得出的数据驱动模型的质量和可传递性。在这里,我们提出了Torchmd,这是具有混合经典和机器学习潜力的分子模拟的框架。所有力计算,包括键,角,二面,Lennard-Jones和库仑相互作用,均以Pytorch阵列和操作表示。此外,Torchmd可以实现学习和模拟神经网络潜力。我们使用标准的琥珀色全原子模拟对其进行验证,学习AB-INITIO潜力,进行端到端训练,最后学习并模拟粗粒的模型以折叠蛋白质。我们认为,Torchmd提供了一个有用的工具集来支持机器学习潜力的分子模拟。代码和数据可在\ url {github.com/torchmd}中免费获得。

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 of 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 \url{github.com/torchmd}.

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