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跨越自由能景观:削减势垒,填充谷值

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys.

作者信息

Fu Haohao, Zhang Hong, Chen Haochuan, Shao Xueguang, Chipot Christophe, Cai Wensheng

机构信息

Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China.

Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071 , China.

出版信息

J Phys Chem Lett. 2018 Aug 16;9(16):4738-4745. doi: 10.1021/acs.jpclett.8b01994. Epub 2018 Aug 7.

Abstract

A robust importance-sampling algorithm for mapping free-energy surfaces over geometrical variables, coined meta-eABF, is introduced. This algorithm shaves the free-energy barriers and floods valleys by incorporating a history-dependent potential term in the extended adaptive biasing force (eABF) framework. Numerical applications on both toy models and nontrivial examples indicate that meta-eABF explores the free-energy surface significantly faster than either eABF or metadynamics (MtD) alone, without the need to stratify the reaction pathway. In some favorable cases, meta-eABF can be as much as five times faster than other importance-sampling algorithms. Many of the shortcomings inherent to eABF and MtD, like kinetic trapping in regions of configurational space already adequately sampled, the requirement of prior knowledge of the free-energy landscape to set up the simulation, are readily eliminated in meta-eABF. Meta-eABF, therefore, represents an appealing solution for a broad range of applications, especially when both eABF and MtD fail to achieve the desired result.

摘要

我们介绍了一种强大的重要性采样算法,用于在几何变量上绘制自由能表面,称为元扩展自适应偏置力(meta-eABF)。该算法通过在扩展自适应偏置力(eABF)框架中纳入一个依赖历史的势项,消除了自由能障碍并填充了低谷。在玩具模型和实际例子上的数值应用表明,meta-eABF比单独的eABF或元动力学(MtD)能更快地探索自由能表面,而无需对反应路径进行分层。在一些有利的情况下,meta-eABF的速度比其他重要性采样算法快五倍之多。eABF和MtD固有的许多缺点,如在已充分采样的构型空间区域中的动力学捕获、设置模拟所需的自由能景观先验知识等,在meta-eABF中都能轻易消除。因此,meta-eABF为广泛的应用提供了一个有吸引力的解决方案,特别是当eABF和MtD都无法达到预期结果时。

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