Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2.
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Hoefinger, Siegfried (2005) Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2. Journal of Computational Chemistry, 26 (11). pp. 1148-1154. ISSN 0192-8651
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.
| Item Type: | Article |
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| Additional Information: | archiving not allowed on institutional repository |
| Keywords: | Poisson-Boltzmann equation; MDGRAPE-2 |
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| Date Deposited: | 14 Dec 2009 13:57 |
| Last Modified: | 14 Dec 2009 13:57 |
| URI: | https://oak.novartis.com/id/eprint/604 |