利用图神经网络实现粗粒度力场的热力学可转移性

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Emily Shinkle, Aleksandra Pachalieva, Riti Bahl, Sakib Matin, Brendan Gifford, Galen T Craven, Nicholas Lubbers
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引用次数: 0

摘要

粗粒度是一种分子建模技术,它以简化的方式表示原子系统,保留对目标输出有贡献的最重要的系统特征,同时去除不那么相关的自由度。与相应的全原子模型相比,降低模型复杂度可使粗粒度分子模拟达到更高的空间和时间尺度。粗粒度分子模拟的一个核心挑战是构建一个力场,在新的表征中以保留原子水平特性的方式表示相互作用。许多构建粗粒度力场的方法由于要对特定热力学状态点的内部波动进行平均,因此在不同热力学条件之间的可转移性有限。在这里,我们使用图卷积神经网络架构--具有张量灵敏度的层次交互粒子神经网络(HIP-NN-TS),开发了一个高度自动化的粗粒度力场训练管道,从而可以研究基于力匹配方法的粗粒度模型的可转移性。我们的研究表明,这种方法不仅能产生高度精确的力场,而且这些力场在各种热力学条件下都更容易转移。这些结果说明了图神经网络等机器学习技术在改进可转移粗粒度力场构建方面的潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.

Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output while removing the degrees of freedom that are less relevant. This reduction in model complexity allows coarse-grained molecular simulations to reach increased spatial and temporal scales compared with corresponding all-atom models. A core challenge in coarse-graining is to construct a force field that represents the interactions in the new representation in a way that preserves the atomistic-level properties. Many approaches to building coarse-grained force fields have limited transferability between different thermodynamic conditions as a result of averaging over internal fluctuations at a specific thermodynamic state point. Here, we use a graph-convolutional neural network architecture, the Hierarchically Interacting Particle Neural Network with Tensor Sensitivity (HIP-NN-TS), to develop a highly automated training pipeline for coarse-grained force fields, which allows for studying the transferability of coarse-grained models based on the force-matching approach. We show that this approach yields not only highly accurate force fields but also that these force fields are more transferable through a variety of thermodynamic conditions. These results illustrate the potential of machine learning techniques, such as graph neural networks, to improve the construction of transferable coarse-grained force fields.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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