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

Published: 1 June 2010| Version 1 | DOI: 10.17632/36kx65gdvw.1
Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, J. Andrew McCammon


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 fast multipole method in which the exponential expansions are used to di... Title of program: AFMPB: Adaptive Fast Multipole Poisson-Boltzmann Solver Catalogue Id: AEGB_v1_0 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



Molecular Biology, Biological Sciences, Computational Physics