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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 Greens 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.
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the n
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory (KSDFT) bas
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from empirical statist
The Poisson-Boltzmann equation (PBE) models the electrostatic interactions of charged bodies such as molecules and proteins in an electrolyte solvent. The PBE is a challenging equation to solve numerically due to the presence of singularities, discon
In numerical simulations of many charged systems at the micro/nano scale, a common theme is the repeated solution of the Poisson-Boltzmann equation. This task proves challenging, if not entirely infeasible, largely due to the nonlinearity of the equa