Accelerating molecular dynamic simulation on graphics processing units - PubMed (original) (raw)

Accelerating molecular dynamic simulation on graphics processing units

Mark S Friedrichs et al. J Comput Chem. 2009.

Abstract

We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.

(c) 2009 Wiley Periodicals, Inc.

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Figures

Figure 1

The set of pxp tiles required for force calculation-only the pink and green tiles need to be calculated. Force data for the grey tiles can be generated by negating the sign of the forces calculated for the corresponding green tile on the other side of the pink diagonal.

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