✦ LIBER ✦

Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods

✍ Scribed by M. E. Davis; J. A. McCammon

Publisher: John Wiley and Sons
Year: 1989
Tongue: English
Weight: 485 KB
Volume: 10
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.540100313

No coin nor oath required. For personal study only.

✦ Synopsis

Comparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite-difference form of the linearized Poisson-Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.

📜 SIMILAR VOLUMES

Solving the finite-difference non-linear

Solving the finite-difference non-linear Poisson–Boltzmann equation

✍ Brock A. Luty; Malcolm E. Davis; J. Andrew McCammon 📂 Article 📅 1992 🏛 John Wiley and Sons 🌐 English ⚖ 375 KB 👁 1 views

## Abstract The Poisson–Boltzmann equation can be used to calculate the electrostatic potential field of a molecule surrounded by a solvent containing mobile ions. The Poisson–Boltzmann equation is a non‐linear partial differential equation. Finite‐difference methods of solving this equation have b

Solving the finite-difference, nonlinear

Solving the finite-difference, nonlinear, Poisson–Boltzmann equation under a linear approach

✍ Xiang Zhexin; Shi Yunyu; Xu Yinwu 📂 Article 📅 1995 🏛 John Wiley and Sons 🌐 English ⚖ 499 KB 👁 1 views

Electrostatic interactions are among the key factors in determining the structure and function of biomolecules. Simulating such interactions involves solving the Poisson equation and the Poisson-Boltzmann (P-B) equation in the molecular interior and exterior region, respectively. The P-B equation is

A two-dimensional stochastic algorithm f

A two-dimensional stochastic algorithm for the solution of the non-linear Poisson–Boltzmann equation: validation with finite-difference benchmarks

✍ Kausik Chatterjee; Jonathan Poggie 📂 Article 📅 2006 🏛 John Wiley and Sons 🌐 English ⚖ 167 KB

The use of conjugate gradients methods w

The use of conjugate gradients methods with a segregated finite volume procedure for solving transient, incompressible Navier-Stokes equations

✍ Nieplocha, J. ;Schreiber, W. C. 📂 Article 📅 1995 🏛 John Wiley and Sons 🌐 English ⚖ 487 KB 👁 2 views

Boundary element solution of the linear

Boundary element solution of the linear Poisson–Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

✍ A. J. Bordner; G. A. Huber 📂 Article 📅 2003 🏛 John Wiley and Sons 🌐 English ⚖ 182 KB 👁 2 views

## Abstract The Poisson–Boltzmann equation is widely used to describe the electrostatic potential of molecules in an ionic solution that is treated as a continuous dielectric medium. The linearized form of this equation, applicable to many biologic macromolecules, may be solved using the boundary e