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用于训练经典和机器学习力场的可逆分子模拟。

Reversible molecular simulation for training classical and machine-learning force fields.

作者信息

Greener Joe G

机构信息

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

出版信息

Proc Natl Acad Sci U S A. 2025 Jun 3;122(22):e2426058122. doi: 10.1073/pnas.2426058122. Epub 2025 May 28.

DOI:10.1073/pnas.2426058122
PMID:40434635
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12146726/
Abstract

The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine-learning potentials. Differentiable molecular simulation calculates gradients of observables with respect to parameters through molecular dynamics trajectories. Here, we improve this approach by explicitly calculating gradients using a reverse-time simulation with effectively constant memory cost and a computation count similar to the forward simulation. The method is applied to learn all-atom water and gas diffusion models with different functional forms and to train a machine-learning potential for diamond from scratch. Comparison to ensemble reweighting indicates that reversible simulation can provide more accurate gradients and train to match time-dependent observables.

摘要

下一代用于分子动力学的力场将利用大量数据来开发。然而,系统地使用实验数据进行训练仍然是一项挑战,特别是对于机器学习势场而言。可微分子模拟通过分子动力学轨迹计算可观测量相对于参数的梯度。在此,我们通过使用反向时间模拟显式计算梯度来改进这种方法,其内存成本有效恒定,计算量与正向模拟相似。该方法被应用于学习具有不同函数形式的全原子水和气体扩散模型,并从零开始训练金刚石的机器学习势场。与系综重加权的比较表明,可逆模拟可以提供更准确的梯度,并训练以匹配与时间相关的可观测量。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/b1a637677edc/pnas.2426058122fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/ec04c0f727d9/pnas.2426058122fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/365a653b2afd/pnas.2426058122fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/381faa8f59ce/pnas.2426058122fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/b1a637677edc/pnas.2426058122fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/ec04c0f727d9/pnas.2426058122fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/365a653b2afd/pnas.2426058122fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/381faa8f59ce/pnas.2426058122fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a35b/12146726/b1a637677edc/pnas.2426058122fig04.jpg

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本文引用的文献

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Refining potential energy surface through dynamical properties via differentiable molecular simulation.通过可微分子模拟利用动力学性质精炼势能面。
Nat Commun. 2025 Jan 18;16(1):816. doi: 10.1038/s41467-025-56061-z.
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Programming patchy particles for materials assembly design.用于材料组装设计的编程补丁颗粒
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