Langevin stabilization of molecular dynamics
Langevin stabilization of molecular dynamics
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DOI：
10.1063/1.1332996
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发表时间：
2001-02-01
影响因子：
4.4
通讯作者：
Skeel, RD
中科院分区：
文献类型：
--
作者：
Izaguirre, JA;Catarello, DP;Skeel, RD
在本文中，我们显示了使用非常温和的随机阻尼的可能性，以稳定牛顿分子动力学的长时间步长积分。更具体地说，稳定和准确的积分获得的阻尼系数，只有百分之几的自然衰减率的过程的利益，如速度自相关函数。本文介绍了两种新的多时间步积分器：Langevin Molly（LM）和Brunger-Brooks-Karplus-Molly（BBK-M）。两者都对牛顿项使用缓和脉冲法。LM使用Langevin方程的离散化，这对恒力是精确的，BBK-M使用流行的Brunger-Brooks-Karplus积分器（BBK）。这些积分器，沿着与外推方法称为LN，在很宽的阻尼系数值范围内进行评估。当使用大阻尼系数时，如溶剂分子的隐式建模，方法LN是上级的，LM紧随其后。然而，在0.2 ps（-1）的温和阻尼下，LM产生最佳结果，允许在包含明确建模的柔性水的模拟中使用14 fs的长时间步长。对于BBK-M和相同的阻尼系数，对于相同的系统，12 fs的时间步长是可能的。对于具有雌激素反应元件ERE的雌激素受体ER的溶剂化蛋白-DNA模拟也获得了类似的结果。BBK-M的并行版本在每个算法上使用最大的稳定时间步长时，运行速度比Verlet-I/r-RWA（可逆参考系统传播算法）快近三倍，并且它也可以很好地并行化。柔性水和ER/ERE的扩散系数的计算表明，当使用高达0.2 ps-1的温和阻尼的动态不显着失真。(C)2001年美国物理学会。
In this paper we show the possibility of using very mild stochastic damping to stabilize long time step integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brunger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps(-1), LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted. (C) 2001 American Institute of Physics.