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Title: AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems

Abstract

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://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.

Authors:
 [1];  [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
981807
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Computer Physics Communications; Journal Volume: 181; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICAL METHODS AND COMPUTING; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ALGORITHMS; A CODES; ELECTROSTATICS; INTEGRAL EQUATIONS; MULTIPOLES; BIOLOGICAL MATERIALS; NUMERICAL SOLUTION

Citation Formats

Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems. United States: N. p., 2010. Web. doi:10.1016/j.cpc.2010.02.015.
Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, & McCammon, Jonathan. AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems. United States. doi:10.1016/j.cpc.2010.02.015.
Lu, Benzhuo, Cheng, Xiaolin, Huang, Jingfang, and McCammon, Jonathan. Fri . "AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems". United States. doi:10.1016/j.cpc.2010.02.015.
@article{osti_981807,
title = {AFMPB: An adaptive fast multipole Poisson Boltzmann solver for calculating electrostatics in biomolecular systems},
author = {Lu, Benzhuo and Cheng, Xiaolin and Huang, Jingfang and McCammon, Jonathan},
abstractNote = {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://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.},
doi = {10.1016/j.cpc.2010.02.015},
journal = {Computer Physics Communications},
number = 6,
volume = 181,
place = {United States},
year = {Fri Jan 01 00:00:00 EST 2010},
month = {Fri Jan 01 00:00:00 EST 2010}
}