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. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field.
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA ; Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA.
Changhao
C
Wang
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
Jun
J
Wang
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA ; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
Qin
Q
Cai
Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA.
Zhilin
Z
Li
Department of Mathematics, University of California, Irvine, CA 92697, USA.
Hong-Kai
HK
Zhao
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA ; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
Ray
R
Luo
Continuum solvent models; Finite difference method; Immersed interface method; Poisson-Boltzmann equation