Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.

ABSTRACT: Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membranes into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their app

SUBMITTER: Botello-Smith WM 

PROVIDER: S-EPMC4720152 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature