Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies

TL;DR

This paper introduces an advanced Poisson-Boltzmann solver, MIBPB, that achieves accurate, robust, and grid size independent electrostatic calculations for solvated molecules, enhancing implicit solvent simulations.

Contribution

The work develops a coarse grid PB solver using Green's function, MIB method, and electrostatic potential extension, improving accuracy and robustness over previous methods.

Findings

MIBPB provides nearly grid size independent reaction field energy calculations.

Numerical tests confirm the robustness and accuracy of MIBPB.

The software accelerates PB solutions through numerical improvements, not hardware.

Abstract

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 online sever.