Solving the Poisson–Boltzmann equation with the specialized computer chip MD-GRAPE-2
✍ Scribed by Siegfried Höfinger
- Publisher
- John Wiley and Sons
- Year
- 2005
- Tongue
- English
- Weight
- 337 KB
- Volume
- 26
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
The accurate description of solvation effects is highly desirable in numerous computational chemistry applications. One widely used methodology treats the solvent as a uniform continuum (“implicit solvation”), and describes its net interaction with the solute by solving the Poisson–Boltzmann (PB) equation using the Boundary Element Method (BEM). These calculations are very time consuming using conventional computers. A new, efficient way of solving the PB equation on the special‐purpose hardware chip MDGRAPE‐2 is presented. The MDGRAPE‐2 chip was originally developed to speed up the calculation of pairwise van der Waals and electrostatic interactions. By recasting the BEM equations and applying an iterative solution procedure, a hardware‐accelerated PB solver on MDGRAPE‐2 could be implemented. The performance and reliability of the method is demonstrated on three examples ranging from small peptides to large proteins, whereby the obtained acceleration factors range from 15‐fold to up to 40‐fold with no loss of accuracy compared to the conventional approach. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1148–1154, 2005