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Harvesting graphics power for MD simulations
Open accessAbstract
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPU's is compared to their main processor counterpart. We achieve speedups of up to 40, 80 and 150 fold, respectively. With the latest generation of GPU's one can run standard MD simulations at 107 flops/$.
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Cited by
Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B., & Lindahl, E. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0018516 · Cited by 940
Borysiuk, V. N., Mochalin, V. N., & Gogotsi, Y. (2015) · Nanotechnology · doi:10.1088/0957-4484/26/26/265705 · Cited by 371
EMMA: A Software Package for Markov Model Building and Analysis
Senne, M., Trendelkamp-Schroer, B., Mey, A. S. J. S., Schütte, C., & Noé, F. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300274u · Cited by 148
Metadata
- Authors
- van Meel, J. A., Arnold, A., Frenkel, D., Portegies Zwart, S. F., & Belleman, R. G.
- Venue
- Molecular Simulation
- Publisher
- Informa UK Limited
- Published
- 2008-03
- Volume
- 34
- Issue
- 3
- Pages
- 259-266
- ISSN
- 0892-7022 (ISSN-L)
- 1029-0435
- OpenAlex
- W2142485291
- Cited by
- 164
- References
- 0
- FWCI
- 47.61
- Type
- journal article
- Language
- en
- Open access
- green
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- van Meel, J. A., Arnold, A., Frenkel, D., Portegies Zwart, S. F., & Belleman, R. G. (2008). Harvesting graphics power for MD simulations. Molecular Simulation. https://doi.org/10.1080/08927020701744295
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