Work

Features of CPB: A P oisson– B oltzmann solver that uses an adaptive cartesian grid

Year: 2014

Type: article

Abstract: The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction-field component (ϕrf ) of the electrostatic potential (ϕ), eliminating the charge-induced singularities in ϕ. CPB can also use a least-squares reconstruction method to improve estimates of ϕ at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ϕ and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson-Boltzmann equation solvers. The reader is referred to http://www.continuum-dynamics.com/solution-mm.html for how to obtain the CPB software.

Source: Journal of Computational Chemistry

DOI: 10.1002/jcc.23791

Authors: Marcia O. Fenley, Robert C. Harris, Travis Mackoy, Alexander H. Boschitsch

Institutions: Florida State University, The University of Texas Medical Branch at Galveston, Duquesne University, Continuum Dynamics (United States)

Language: English

Topic: Advanced Chemical Physics Studies

Subfield: Atomic and Molecular Physics, and Optics

Field: Physics and Astronomy

Domain: Physical Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute of General Medical Sciences

Awards: Advanced Electrostatic Computation in Molecular Dynamics, Advanced Electrostatic Computation in Molecular Dynamics