AFMPB：一种用于计算生物分子系统静电学的自适应快速多极泊松-玻尔兹曼求解器
AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems.
作者信息
Lu Benzhuo, Cheng Xiaolin, Huang Jingfang, McCammon J Andrew
机构信息
State Key Laboratory of Scientific/Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100910, China.
出版信息
Comput Phys Commun. 2010 Jun 1;181(6):1150-1160. doi: 10.1016/j.cpc.2010.02.015.
A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole to local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.
介绍了一个Fortran程序包，用于快速评估由线性化泊松-玻尔兹曼方程建模的生物分子系统中的静电势和力。数值求解器采用了条件良好的边界积分方程（BIE）公式、节点面片离散化方案、具有反向通信协议的 Krylov 子空间迭代求解器包，以及一种自适应的新版本快速多极方法，其中使用指数展开来对角化多极到局部平移。该程序及其完整描述，以及几个密切相关的库和实用工具可在http://lsec.cc.ac.cn/lubz/afmpb.html以及http://mccammon.ucsd.edu/的镜像站点获取。本文是该程序的简要总结：算法、实现和用法。
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