Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations
Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations
复制标题
生物大分子模拟中计算静电相互作用的快速多极方法的性能
DOI：
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发表时间：
1994
影响因子：
3
通讯作者：
T. Takada
中科院分区：
文献类型：
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作者：
J. Shimada;H. Kaneko;T. Takada
Greengard和Rokhlin （GR）提出的快速多极子方法适用于大型生物大分子体系。该方法将系统划分为分层单元，并将施加在粒子上的电场分解为两部分。第一部分是由于附近的细胞而快速变化的场，因此需要严格的两两计算。第二部分是由于远处细胞的影响而缓慢变化的局部场；因此，它可以通过多极展开技术进行快速计算。在这项工作中，对另外两种提高性能的可能性进行了数值研究。第一个是通过增加附近单元的数量来改善膨胀的收敛性，而不包括高阶多极矩。二是粒子-粒子和粒子-网格/多极展开（PPPM/MPE）方法加速了计算，该方法采用快速傅里叶变换代替了层次结构。为此，将作者最初针对周期系统开发的PPPM/MPE方法推广到非周期孤立系统。讨论了周期系统和孤立系统的GR和PPPM/MPE方法的优缺点。数值计算表明，这些方法在合理的成本下，可以将每个粒子感受到的电位误差降低到0.1-1 kcal/mol，远远小于传统简单截断所涉及的30 - kcal/mol误差。©1994 by John Wiley & Sons, Inc。
The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher‐order multipole moments. The second is an acceleration of the calculations by the particle–particle and particle–mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1–1 kcal/mol, much smaller than the 30‐kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.