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

DOI10.1016/j.cpc.2010.02.015zbMath1220.78002OpenAlexW2008246496WikidataQ33598495 ScholiaQ33598495MaRDI QIDQ5892500

Jingfang Huang, Benzhuo Lu, J. Andrew McCammon, Xiaolin Cheng

Publication date: 31 May 2011

Published in: Computer Physics Communications (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.cpc.2010.02.015

zbMATH Keywords

boundary integral equationKrylov subspace methodsPoisson-Boltzmann equationfast multipole methodsdiagonal translationsnode-patch methodsoftware tool \texttt{AFMPB}

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Software, source code, etc. for problems pertaining to optics and electromagnetic theory (78-04) Multipole methods applied to problems in optics and electromagnetic theory (78M16)

Related Items (11)

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ Model reduction-based initialization methods for solving the Poisson-Nernst-Planck equations in three-dimensional ion channel simulations ⋮ Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy ⋮ A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules ⋮ Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation ⋮ Unnamed Item ⋮ A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule ⋮ A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models ⋮ DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture ⋮ A Fourier-series-based kernel-independent fast multipole method ⋮ Progress in developing Poisson-Boltzmann equation solvers

Uses Software

• APBS
• AFMPB

Cites Work

• Unnamed Item
• Unnamed Item
• FMM-Yukawa: an adaptive fast multipole method for screened Coulomb interactions
• A new version of the fast multipole method for screened Coulomb interactions in three dimensions
• Solution of acoustic scattering problems by means of second kind integral equations
• The electric potential of a macromolecule in a solvent: A fundamental approach
• A fast adaptive multipole algorithm in three dimensions
• GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems
• A fast algorithm for particle simulations

This page was built for publication: AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems