Fast version of the structure adapted multipole method-efficient calculation of electrostatic forces in protein dynamics

被引:34
|
作者
Niedermeier, C [1 ]
Tavan, P [1 ]
机构
[1] UNIV MUNICH,INST MED OPT,D-80333 MUNICH,GERMANY
关键词
molecular dynamics; protein dynamics; electrostatic forces; hierarchical multipole methods; structure adaptivity;
D O I
10.1080/08927029608024094
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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%.
引用
收藏
页码:57 / 66
页数:10
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