Jung Jaewoon, Mori Takaharu, Sugita Yuji
Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
J Comput Chem. 2013 Oct 30;34(28):2412-20. doi: 10.1002/jcc.23404. Epub 2013 Aug 12.
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.
生物分子分子动力学（MD）模拟中的主要瓶颈在于诸如 Lennard-Jones 等成对非键相互作用以及长程静电相互作用的计算。粒子网格埃瓦尔德（PME）方法能够在 MD 模拟期间准确且快速地评估长程静电相互作用。然而，能量和梯度的评估包含耗时的平方根倒数和互补误差函数。为了在保持准确性的同时避免此类耗时操作，我们通过将能量和梯度定义为距离平方倒数的线性函数，提出了一种用于 PME 中短程相互作用的新查找表。在我们的查找表方法中，表点密度与成对距离的平方成反比，从而能够在小成对距离下准确评估能量和梯度。尽管此处存在逆运算，但由于有效利用了高速缓存存储器，新的查找表方案允许进行快速的成对非键计算。
