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 GPUs is compared to their main processor counterpart. We achieve speedups of up to 40, 80 and 150 fold, respectively. With the latest generation of GPUs one can run standard MD simulations at 107 flops/$.

dx.doi.org/10.1080/08927020701744295
Mol. Simul.

van Meel, J. A, Arnold, A, Frenkel, D, Portegies Zwart, S. F, & Belleman, R. G. (2008). Harvesting graphics power for MD simulations. Mol. Simul., 34, 259–266. doi:10.1080/08927020701744295