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

Published: 1 November 2013| Version 1 | DOI: 10.17632/444yd7f7rd.1
Contributors:
Benzhuo Lu,
Xiaolin Cheng,
Jingfang Huang,
J. Andrew McCammon

Description

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) 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 the fast multipole method in which the exponential expansions are used t... Title of program: AFMPB Catalogue Id: AEGB_v1_1 Nature of problem Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Versions of this program held in the CPC repository in Mendeley Data AEGB_v1_0; AFMPB: Adaptive Fast Multipole Poisson-Boltzmann Solver; 10.1016/j.cpc.2010.02.015 AEGB_v1_1; AFMPB; 10.1016/j.cpc.2013.05.012 AEGB_v2_0; Parallel AFMPB; 10.1016/j.cpc.2014.12.022

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Molecular Biology, Biological Sciences, Computational Physics

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