Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2.
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.
Höfinger
Siegfried
S
IK@N, ISS, Novartis Institutes for Biomedical Research GmbH, Brunner Strasse 59, A-1235 Wien, Austria. siegfried.hoefinger@novartis.com
D000465:Algorithms; D019732:Amide Synthases / Q000737:chemistry; D002480:Cellulase / Q000737:chemistry; D008555:Melitten / Q000737:chemistry; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins; D008555:Melitten; D002480:Cellulase; D019732:Amide Synthases; C038479:NAD+ synthase