Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
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DOI：
10.1016/j.cpc.2013.10.006
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发表时间：
2014-02-01
影响因子：
6.3
通讯作者：
Farago, Oded
中科院分区：
文献类型：
--
作者：
Gronbech-Jensen, Niels;Hayre, Natha Robert;Farago, Oded
一个新的Langevin-Verlet恒温器，保留离散时间步长的波动耗散关系的分子建模和测试对几个流行的套件（琥珀，GROMACS，LAMMPS）使用一个小分子作为一个例子，可以很容易地模拟所有三个包。与现有的方法相反，新的恒温器表现出没有检测到的变化，在采样统计的时间步长是在整个数值稳定范围内变化。该方法的简单形式，我们表示在三种常见的形式（速度显式，Stormer-Verlet，和跳蛙），允许在现有的分子模拟软件包中轻松实现，以实现更快，更准确的结果，没有成本的计算时间或编程复杂性。(C)2013 Elsevier B. V.保留所有权利。
A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Stormer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity. (C) 2013 Elsevier B.V. All rights reserved.