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

Journal Article · Fri Jan 01 00:00:00 EST 2010 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2010.02.015· OSTI ID:981807

Lu, Benzhuo ^[1]; Cheng, Xiaolin ^[1]; Huang, Jingfang ^[1]; McCammon, Jonathan ^[1]

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1. ORNL

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 981807
• Journal Information: Computer Physics Communications, Vol. 181, Issue 6; ISSN 0010-4655
• Country of Publication: United States
• Language: English

Related Subjects

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