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Harvesting graphics power for MD simulations

By J.A. van Meel, A. Arnold, D. Frenkel, S.F. Portegies Zwart and R.G. Belleman


We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA\ud CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms\ud suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The\ud performance of the GPU’s is compared to their main processor counterpart. We achieve speedups of up to 40, 80 and 150\ud fold, respectively. With the latest generation of GPU’s one can run standard MD simulations at 107 flops/$

Topics: Scheikunde, molecular dynamics simulation, GPGPU, random number generator
Year: 2008
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