Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

Molecular dynamics is an important computational tool to simulate and understand biochemical processes at the atomic level. However, accurate simulation of processes such as protein folding requires a large number of both atoms and time steps. This in turn leads to huge runtime requirements. Hence,...

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Bibliographic Details
Published in:Computer physics communications 2008-11, Vol.179 (9), p.634-641
Main Authors: Liu, Weiguo, Schmidt, Bertil, Voss, Gerrit, Müller-Wittig, Wolfgang
Format: Article
Language:English
Subjects:
Advanced computer architecture
Graphics processing unit
Molecular dynamics
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Summary:Molecular dynamics is an important computational tool to simulate and understand biochemical processes at the atomic level. However, accurate simulation of processes such as protein folding requires a large number of both atoms and time steps. This in turn leads to huge runtime requirements. Hence, finding fast solutions is of highest importance to research. In this paper we present a new approach to accelerate molecular dynamics simulations with inexpensive commodity graphics hardware. To derive an efficient mapping onto this type of computer architecture, we have used the new Compute Unified Device Architecture programming interface to implement a new parallel algorithm. Our experimental results show that the graphics card based approach allows speedups of up to factor nineteen compared to the corresponding sequential implementation.
ISSN:0010-4655
1879-2944
DOI:10.1016/j.cpc.2008.05.008