A Novel Charge Distribution Method for the Numerical Solution of the Poisson-Boltzmann Equation
- Resource Type
- Authors
- Jium‐Tyne Pan; Wen-Jiun Peng; Thy-Hou Lin
- Source
- Journal of the Chinese Chemical Society. 43:7-16
- Subject
- Chemistry
Point particle
Mathematical analysis
Finite difference method
Charge density
Charge (physics)
General Chemistry
Poisson–Boltzmann equation
Grid
symbols.namesake
Electric field
symbols
Van der Waals radius
Atomic physics
Computer Science::Distributed, Parallel, and Cluster Computing
- Language
- ISSN
- 0009-4536
A charge distribution method to solve the linearized Poisson-Boltzmann equation numerically through use of the finite difference method is proposed, The molecules are mapped by 1 and 0.25 A grid systems. Each atom is modeled as a point charge and a weighted sum of point charge of every atom that is within its van der Waals radius with a grid point is assigned to the grid point. Depending on a charge distribution factor determined, the charge/grid (q/g) ratio calculated for every grid point inside a molecule can be fixed to a certain value. A grid size of the I A grid is often fixed for mapping a small or large molecular system. Solvation energies for a group of small molecules calculated by the method arc comparable with those calculated by other methods and the grid energy calculated by the method is also reduced.