Calculating potentials of mean force from steered molecular dynamics simulations
Calculating potentials of mean force from steered molecular dynamics simulations
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DOI：
10.1063/1.1651473
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发表时间：
2004-04-01
影响因子：
4.4
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Park, S;Schulten, K
操纵分子动力学（SMD）允许有效的调查分子过程，集中在选定的自由度。我们解释如何可以，在SMD的框架内，采用Jarzynski的等式（也称为非平衡功关系）来计算平均力（PMF）的潜力。我们概述了服务于这一目的的理论，并将非平衡过程（如SMD模拟）与平衡性质（如PMF）联系起来。我们回顾推导Jarzynski的平等，将其推广到等压等温过程，并讨论其影响的热力学第二定律和计算机模拟。在相关制度的指导，通过刚性弹簧，我们证明了系统上的工作是高斯分布的速度的过程模拟无关。在这种情况下，Jarzynski等式的累积展开可以安全地终止于二阶。我们说明了PMF计算方法的一个示例性的模拟，并证明了高斯性质的工作分布。(C)2004年，美国物理学会。
Steered molecular dynamics (SMD) permits efficient investigations of molecular processes by focusing on selected degrees of freedom. We explain how one can, in the framework of SMD, employ Jarzynski's equality (also known as the nonequilibrium work relation) to calculate potentials of mean force (PMF). We outline the theory that serves this purpose and connects nonequilibrium processes (such as SMD simulations) with equilibrium properties (such as the PMF). We review the derivation of Jarzynski's equality, generalize it to isobaric-isothermal processes, and discuss its implications in relation to the second law of thermodynamics and computer simulations. In the relevant regime of steering by means of stiff springs, we demonstrate that the work on the system is Gaussian-distributed regardless of the speed of the process simulated. In this case, the cumulant expansion of Jarzynski's equality can be safely terminated at second order. We illustrate the PMF calculation method for an exemplary simulation and demonstrate the Gaussian nature of the resulting work distribution. (C) 2004 American Institute of Physics.