Fast Version of the Structure Adapted Multipole Method–Efficient Calculation of Electrostatic Forces in Protein Dynamics
Fast Version of the Structure Adapted Multipole Method–Efficient Calculation of Electrostatic Forces in Protein Dynamics
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结构适应多极方法的快速版本——蛋白质动力学中静电力的高效计算
DOI：
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发表时间：
1996
期刊：
影响因子：
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通讯作者：
P. Tavan
中科院分区：
文献类型：
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作者：
C. Niedermeier;P. Tavan
蛋白质分子动力学模拟中静电力计算的传统算法对于N个原子的体系需要O（N2）量级的计算工作。截断法，试图避免这种努力，需要在力，能量和其他可观察到的不可容忍的大错误。分层多极方法允许快速和正确的静电力的评估。我们描述了一个改进版本的结构自适应多极子方法（SAMM），它不仅规模与O（N），但也一样快截断算法。与后者不同的是，它能够以低于1%的误差再现静电力。
Abstract Traditional algorithms for evaluation of electrostatic forces in molecular dynamics simulations of proteins require computational work of the order O(N 2) for a system of N atoms. Truncation methods, which try to avoid that effort, entail intolerably large errors in forces, energies and other observables. Hierarchical multipole methods allow rapid and correct evaluation of electrostatic forces. We describe an improved version of the Structure Adapted Multipole Method (SAMM) which not only scales with O(N) but also works as fast as truncation algorithms. Unlike the latter it manages to reproduce electrostatic forces with an error below 1%.