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自适应单副本多状态转换接口采样。

Adaptive single replica multiple state transition interface sampling.

机构信息

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.

出版信息

J Chem Phys. 2013 Jul 28;139(4):044105. doi: 10.1063/1.4813777.

Abstract

The multiple state transition path sampling method allows sampling of rare transitions between many metastable states, but has the drawback that switching between qualitatively different pathways is difficult. Combination with replica exchange transition interface sampling can in principle alleviate this problem, but requires a large number of simultaneous replicas. Here we remove these drawbacks by introducing a single replica sampling algorithm that samples only one interface at a time, while efficiently walking through the entire path space using a Wang-Landau approach or, alternatively, a fixed bias. We illustrate the method on several model systems: a particle diffusing in a simple 2D potential, isomerization in a small Lennard Jones cluster, and isomerization of the alanine dipeptide in explicit water.

摘要

多态跃迁路径采样方法允许对许多亚稳态之间的罕见跃迁进行采样,但存在一个缺点,即不同质的途径之间的转换很困难。与复制交换跃迁界面采样相结合原则上可以缓解这个问题,但需要大量的同时复制。在这里,我们通过引入一种仅一次采样一个界面的单复制采样算法来消除这些缺点,同时使用 Wang-Landau 方法或固定偏差有效地遍历整个路径空间。我们在几个模型系统上演示了该方法:在简单的 2D 势中扩散的粒子、小 Lennard-Jones 团簇中的异构化以及在明水中的丙氨酸二肽的异构化。

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