A special purpose computer for molecular dynamics calculations
Journal of Computational Physics
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Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Parallel implementation of a molecular dynamics simulation program
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SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
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The Journal of Supercomputing
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MMCP'11 Proceedings of the 2011 international conference on Mathematical Modeling and Computational Science
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system
Journal of Parallel and Distributed Computing
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Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) to design and implement a new parallel algorithm. This results in an implementation with significant runtime savings on an off-the-shelf computer graphics card.