APBS 0.4.0 User Guide: Adaptive Poisson-Boltzmann Solver
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Introduction

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

APBS uses PMG to solve the Poisson-Boltzmann equation numerically. PMG is developed and maintained by the Holst Research Group at UC San Diego, and is designed to solve the nonlinear Poisson-Boltzmann equation and similar problems with linear space and time complexity through the use of box methods, inexact Newton methods, and algebraic multilevel methods. More information about PMG may be found at http://www.fetk.org.

APBS also uses FEtk to solve the Poisson-Boltzmann equation numerically. FEtk is developed and maintained by the Holst Research Group at UC San Diego, and is designed to solve general coupled systems of nonlinear partial differential equations accurately and efficiently using adaptive multilevel finite element methods, inexact Newton methods, algebraic multilevel methods. More information about FEtk may be found at http://www.fetk.org.

Financial support. The development of APBS has been supported financially by:

Citing APBS. Please acknowledge your use of APBS by citing:

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98, 10037-10041, 2001.

Citing FEtk and PMG. Please acknowledge your use of PMG and FEtk by citing:

M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem., 14 (1993), pp. 105-113.

M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem., 16 (1995), pp. 337-364.

M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191.

R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review, 45 (2003), pp. 291-323.

Contributing authors. APBS was primarily written by Nathan Baker during his graduate work with J. Andrew McCammon and Michael Holst and extensively developed over the subsequent years. APBS uses several libraries written by Mike Holst and members of the Holst group, including: PMG (multigrid solver for Cartesian mesh discretization), FEtk (provides finite element framework, error estimators, and solvers), and MALOC (hardware abstraction library for code portability). Additionally, a number of people have made important contributions to enhance APBS functionality and usability. The full author list (in alphabetical order) is:

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APBS 0.4.0 User Guide Installation