Accelerated Molecular Dynamics Methods: Introduction and Recent Developments
Accelerated Molecular Dynamics Methods: Introduction and Recent Developments
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DOI：
10.1016/s1574-1400(09)00504-0
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发表时间：
2009-01-01
期刊：
影响因子：
--
通讯作者：
Voter, Arthur F.
中科院分区：
文献类型：
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作者：
Perez, Danny;Uberuaga, Blas P.;Voter, Arthur F.
由于其无与伦比的预测能力，分子动力学（MD）方法被广泛应用于理论化学，物理学，生物学，材料科学和工程。然而，由于计算成本，MD模拟只能用于直接模拟有限时间尺度上的动态过程（例如，纳秒或至多几微秒），即使非平衡过程的模拟通常可能需要显著更长的时间尺度，特别是当它们涉及热激活时。在本文中，我们提出了一个介绍加速分子动力学，一类方法，旨在延长分子动力学的时间尺度范围，有时高达秒或更长。支持不同方法的理论基础（平行副本动力学，超动力学和温度加速动力学）首先进行了讨论。然后，我们讨论了一些应用和最新进展，包括超状态并行副本动力学，自学习超动力学，空间并行温度加速动力学。
Because of its unrivaled predictive power, the molecular dynamics (MD) method is widely used in theoretical chemistry, physics, biology, materials science, and engineering. However, due to computational cost, MD simulations can only be used to directly simulate dynamical processes over limited timescales (e.g., nanoseconds or at most a few microseconds), even though the simulation of nonequilibrium processes can often require significantly longer timescales, especially when they involve thermal activation. In this paper, we present an introduction to accelerated molecular dynamics, a class of methods aimed at extending the timescale range of molecular dynamics, sometimes up to seconds or more. The theoretical foundations underpinning the different methods (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) are first discussed. We then discuss some applications and recent advances, including super-state parallel replica dynamics, self-learning hyperdynamics, and spatially parallel temperature-accelerated dynamics.