Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson-Boltzmann equation for electrostatic analyses of realistic bio-molecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules.

Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision with Finite-Difference Algorithms.

Violation of energy conservation in Poisson-Boltzmann molecular dynamics, due to the limited accuracy and precision of numerical methods, is a major bottleneck preventing its wide adoption in biomolecular simulations. We explored the ideas of enforcing interface conditions by the immerse interface method and of removing charge singularity to improve the finite-difference methods. Our analysis of these ideas on an analytical test system shows significant improvement in both energies and forces.

On removal of charge singularity in Poisson-Boltzmann equation.

The Poisson-Boltzmann theory has become widely accepted in modeling electrostatic solvation interactions in biomolecular calculations. However the standard practice of atomic point charges in molecular mechanics force fields introduces singularity into the Poisson-Boltzmann equation. The finite-difference/finite-volume discretization approach to the Poisson-Boltzmann equation alleviates the numerical difficulty associated with the charge singularity but introduces discretization error into the electrostatic potential.