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:
-
- 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
- Journal Name:
- Computer Physics Communications
- Additional Journal Information:
- Journal Volume: 181; Journal Issue: 6; Journal ID: ISSN 0010-4655
- 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. https://doi.org/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. https://doi.org/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},
url = {https://www.osti.gov/biblio/981807},
journal = {Computer Physics Communications},
issn = {0010-4655},
number = 6,
volume = 181,
place = {United States},
year = {2010},
month = {1}
}