Efficient Lookup Table Using a Linear Function of Inverse Distance Squared
Efficient Lookup Table Using a Linear Function of Inverse Distance Squared
复制标题
DOI：
10.1002/jcc.23404
复制
发表时间：
2013-10-30
影响因子：
3
通讯作者：
Sugita, Yuji
中科院分区：
文献类型：
--
作者：
Jung, Jaewoon;Mori, Takaharu;Sugita, Yuji
生物分子的分子动力学（MD）模拟的主要瓶颈存在于Lennard-Jones和长程静电相互作用等成对非键相互作用的计算中。在分子动力学模拟中，粒子网格埃瓦尔德（PME）方法能够准确、快速地计算长程静电相互作用。然而，能量和梯度的评估包括耗时的平方根倒数和互补误差函数。为了避免这种耗时的操作，同时保持准确性，我们提出了一个新的查找表，在PME的短程相互作用，通过定义能量和梯度作为距离平方反比的线性函数。在我们的查找表方法中，表点的密度与成对距离的平方成反比，从而能够在较小的成对距离处准确评估能量和梯度。不管这里的逆操作，新的查找表方案允许快速成对非绑定计算，由于高速缓存存储器的有效使用。(c)2013 Wiley Periodicals，Inc.
The major bottleneck in molecular dynamics (MD) simulations of biomolecules exist in the calculation of pairwise nonbonded interactions like Lennard-Jones and long-range electrostatic interactions. Particle-mesh Ewald (PME) method is able to evaluate long-range electrostatic interactions accurately and quickly during MD simulation. However, the evaluation of energy and gradient includes time-consuming inverse square roots and complementary error functions. To avoid such time-consuming operations while keeping accuracy, we propose a new lookup table for short-range interaction in PME by defining energy and gradient as a linear function of inverse distance squared. In our lookup table approach, densities of table points are inversely proportional to squared pair distances, enabling accurate evaluation of energy and gradient at small pair distances. Regardless of the inverse operation here, the new lookup table scheme allows fast pairwise nonbonded calculations owing to efficient usage of cache memory. (c) 2013 Wiley Periodicals, Inc.