Longer time steps for molecular dynamics
Longer time steps for molecular dynamics
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DOI：
10.1063/1.478995
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发表时间：
1999-05-22
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;Reich, S;Skeel, RD
生物分子动力学的模拟已经通过使用多个时间步进方法大大加速，例如Verlet-I/r-RWA（可逆参考系统传播算法）方法，其基于将“慢”力近似为广泛分离的脉冲。事实上，数值实验表明，4 fs的时间步长是可能的，这些缓慢的力量，但不幸的是，也表明，5 fs的长时间步长的结果在一个戏剧性的能量漂移。为了克服这种不稳定性，一个辛修改的脉冲Verlet-I/r-RWA方法已被提出，称为软化脉冲方法。其思想是，修改势能的慢部分，使其以位置的“时间平均”值进行评估，并将此修改后的势能的梯度用于力的慢部分。通过过滤掉最快运动的激励，这些平均值允许使用比脉冲方法更长的时间步长。我们介绍了一种新的缓和方法，平衡，避免不稳定性，在一个更有效的方式比以前的平均缓和方法。实验结果表明，时间步长为6 fs的Equilibrium方法与时间步长为4 fs的脉冲Verlet-I/r-A方法一样稳定.我们表明，它可能是必要的，包括非粘结力的影响，在平均，使更长的时间步长可能。我们还表明，轻微的修改的潜力有很小的影响精度。为了这个目的，我们比较自扩散系数和径向分布函数对蛙跳方法与短的时间步长（0.5 fs）。(C)1999年美国物理学会。[S0021-9606（99）01520-2]。
Simulations of the dynamics of biomolecules have been greatly accelerated by the use of multiple time-stepping methods, such as the Verlet-I/r-RESPA (reversible reference system propagator algorithms) method, which is based on approximating "slow'' forces as widely separated impulses. Indeed, numerical experiments have shown that time steps of 4 fs are possible for these slow forces but unfortunately have also shown that a long time step of 5 fs results in a dramatic energy drift. To overcome this instability, a symplectic modification of the impulsive Verlet-I/r-RESPA method has been proposed, called the mollified impulse method. The idea is that one modifies the slow part of the potential energy so that it is evaluated at "time averaged'' values of the positions, and one uses the gradient of this modified potential for the slow part of the force. By filtering out excitations to the fastest motions, these averagings allow the use of longer time steps than does the impulse method. We introduce a new mollified method, Equilibrium, that avoids instability in a more effective manner than previous averaging mollified methods. Our experiments show that Equilibrium with a time step of 6 fs is as stable as the impulsive Verlet-I/r-RESPA method with a time step of 4 fs. We show that it may be necessary to include the effect of nonbonded forces in the averaging to make yet longer time steps possible. We also show that the slight modification of the potential has little effect on accuracy. For this purpose we compare self-diffusion coefficients and radial distribution functions against the Leapfrog method with a short time step (0.5 fs). (C) 1999 American Institute of Physics. [S0021-9606(99)01520-2].