Accurate, robust and reliable calculations of Poisson-Boltzmann
B. Wang, and G. Wei. (2016)cite arxiv:1607.04594Comment: 15 pages, 3 figures.
Developing accurate solvers for the Poisson Boltzmann (PB) model is the first
step to make the PB model suitable for implicit solvent simulation. Reducing
the grid size influence on the performance of the solver benefits to increasing
the speed of solver and providing accurate electrostatics analysis for solvated
molecules. In this work, we explore the accurate coarse grid PB solver based on
the Green's function treatment of the singular charges, matched interface and
boundary (MIB) method for treating the geometric singularities, and posterior
electrostatic potential field extension for calculating the reaction field
energy. We made our previous PB software, MIBPB, robust and provides almost
grid size independent reaction field energy calculation. Large amount of the
numerical tests verify the grid size independence merit of the MIBPB software.
The advantage of MIBPB software directly make the acceleration of the PB solver
from the numerical algorithm instead of utilization of advanced computer
architectures. Furthermore, the presented MIBPB software is provided as a free