Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration
Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration
复制标题
将无迭代偏振与大时间步随机等速积分相结合
DOI：
10.1021/acs.jctc.9b00072
复制
发表时间：
2019
影响因子：
5.5
通讯作者：
Head-Gordon, Teresa
中科院分区：
文献类型：
--
作者：
Albaugh, Alex;Tuckerman, Mark E.;Head-Gordon, Teresa
为了加速使用可极化力场的分子动力学模拟，我们结合了一种新的扩展拉格朗日方法(IEL/0-SCF)和一种允许使用多时间尺度算法(SIN(R))的长时间步长的随机积分方案。我们考虑了将非键力的不同分量放入不同的时间尺度的组合格式的不同算法，以及在时间尺度上拆分单个非键力的不同算法，以证明组合方法不仅适用于大量水，也适用于浓缩的盐溶液、水溶液、多肽和溶剂化蛋白质。根据系统和所需精度的不同，IEL/0-SCF和SIN(R)的组合相对于使用参考程序Tingker 8.1中实现的标准SCF求解器的分子动力学Verlet积分，产生了∼6-8的较低的计算速度。这种组合的方法体现了在多体势能面的正则系综中的平衡模拟的重大进步，其速度超过了单独使用这两种方法所能达到的速度。
In order to accelerate molecular dynamics simulations using polarizable force fields, we combine a new extended Lagrangian approach that eliminates the self-consistent field step (iEL/0-SCF) with a stochastic integration scheme that allows for a long time step using a multiple time scale algorithm (SIN(R)). We consider different algorithms for the combined scheme that places different components of the nonbonded forces into different time scales, as well as splitting individual nonbonded forces across time scales, to demonstrate that the combined method works well for bulk water as well as for a concentrated salt solution, aqueous peptide, and solvated protein. Depending on system and desired accuracy, the iEL/0-SCF and SIN(R) combination yields lower bound computational speed-ups of ∼6–8 relative to a molecular dynamics Verlet integration using a standard SCF solver implemented in the reference program TINKER 8.1. The combined approach embodies a significant advance for equilibrium simulations in the canonical ensemble of many-body potential energy surfaces for condensed phase systems with speed-ups that exceed what is possible by either method alone.