Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson鈥揃oltzmann Equation

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• 作者：Wesley M. Botello-Smith ; Ray Luo
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2015
• 出版时间：October 26, 2015
• 年：2015
• 卷：55
• 期：10
• 页码：2187-2199
• 全文大小：658K
• ISSN：1549-960X

文摘

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鈥揃oltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson鈥揃oltzmann 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 applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multigrid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations.