Molecular dynamics simulations on commodity gpus with cuda

Abstract. Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treat-ment 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 process-ing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and moti-vated 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 de-sign and implement a new parallel algorithm. This results in an imple-mentation with significant runtime savings on an off-the-shelf computer graphics card.