Fast evaluation of polarizable forces
Fast evaluation of polarizable forces
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DOI：
10.1063/1.2056544
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发表时间：
2005-10-22
影响因子：
4.4
通讯作者：
Skeel, RD
中科院分区：
文献类型：
--
作者：
Wang, W;Skeel, RD
极化性被认为是下一代生物分子模拟力场中最重要的发展。然而，由于在模拟的每个步骤中求解大型密集线性系统的成本，极化力场中感应原子偶极子的自洽计算是昂贵的。本文介绍了一些方法，可将计算可极化模型的静电能和力的成本从计算非极化模型的成本的约 7.5 倍降低到不到两倍。这可能足以满足生物分子模拟中极化力的常规使用。计算时间的减少是通过粒子网格 Ewald 方法的有效实现实现的，该方法是基于最小二乘拟合的精确且鲁棒的预测器，以及通过简单的预处理器加速快速收敛的非平稳迭代方法。此外，通过这些方法，具有较大时间步长的自洽方法比扩展拉格朗日方法更快。使用先前时间步长的偶极矩来计算迭代方法的准确初始猜测会导致能量漂移，该漂移可以做得很小，可以接受。如果对迭代施加相当严格的收敛标准，则使用零初始猜测不会导致可察觉的能量漂移。 (c) 2005 年美国物理研究所。
Polarizability is considered to be the single most significant development in the next generation of force fields for biomolecular simulations. However, the self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense linear system at each step of a simulation. This article introduces methods that reduce the cost of computing the electrostatic energy and force of a polarizable model from about 7.5 times the cost of computing those of a nonpolarizable model to less than twice the cost. This is probably sufficient for the routine use of polarizable forces in biomolecular simulations. The reduction in computing time is achieved by an efficient implementation of the particle-mesh Ewald method, an accurate and robust predictor based on least-squares fitting, and non-stationary iterative methods whose fast convergence is accelerated by a simple preconditioner. Furthermore, with these methods, the self-consistent approach with a larger timestep is shown to be faster than the extended Lagrangian approach. The use of dipole moments from previous timesteps to calculate an accurate initial guess for iterative methods leads to an energy drift, which can be made acceptably small. The use of a zero initial guess does not lead to perceptible energy drift if a reasonably strict convergence criterion for the iteration is imposed. (c) 2005 American Institute of Physics.