Cell multipole method for molecular simulations in bulk and confined systems
Cell multipole method for molecular simulations in bulk and confined systems
复制标题
用于本体和受限系统中分子模拟的单元多极方法
DOI：
10.1063/1.1553979
复制
发表时间：
2003
影响因子：
4.4
通讯作者：
Shaoyi Jiang
中科院分区：
文献类型：
--
作者：
Jie Zheng;R. Balasundaram;S. Gehrke;G. Heffelfinger;W. Goddard;Shaoyi Jiang
分子模拟的瓶颈之一是处理涉及静电相互作用的大系统。在传统的分子模拟方法中，计算时间与O（N{sup 2}）成比例，其中N是原子的数量。随着细胞多极方法（CMM）和大规模并行超级计算机的出现，已经进行了1000万个原子的模拟。为快速准确地模拟三维体系，提出了最佳层次单元和泰勒展开算法。CMM扩展到处理准二维系统，这对凝聚态物理问题非常重要。此外，CMM被应用到巨正则系综蒙特卡罗（GCMC）模拟的3D和2D系统。在最优条件下，计算结果表明，对于大系统，计算时间与N近似成线性关系，总势能的平均误差小于1%，与Ewald求和法相比，三维和二维系统的均方根力约为0.015。
One of the bottlenecks in molecular simulations is to treat large systems involving electrostatic interactions. Computational time in conventional molecular simulation methods scales with O(N{sup 2}), where N is the number of atoms. With the emergence of the cell multipole method (CMM) and massively parallel supercomputers, simulations of 10 million atoms have been performed. In this work, the optimal hierarchy cell level and the algorithm for Taylor expansion were recommended for fast and accurate molecular dynamics (MD) simulations of three-dimensional (3D) systems. CMM was then extended to treat quasi-two-dimensional (2D) systems, which is very important for condensed matter physics problems. In addition, CMM was applied to grand canonical ensemble Monte Carlo (GCMC) simulations for both 3D and 2D systems. Under the optimal conditions, the results show that computational time is approximately linear with N for large systems, average error in total potential energy is less than {approx}1%, and RMS force is about 0.015 for 3D and 2D systems when compared with the Ewald summation.