A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software
✍ Scribed by Nathan Schmid; Mathias Bötschi; Wilfred F. Van Gunsteren
- Book ID
- 102305812
- Publisher
- John Wiley and Sons
- Year
- 2010
- Tongue
- English
- Weight
- 191 KB
- Volume
- 31
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
Abstract
During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010