Molecular Dynamics Simulations on Commodity GPUs with CUDA

@incollection{citeulike:2453098, abstract = {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.}, author = {Liu, Weiguo and Schmidt, Bertil and Voss, Gerrit and M\"{u}ller-Wittig, Wolfgang }, citeulike-article-id = {2453098}, doi = {10.1007/978-3-540-77220-0\_20}, journal = {High Performance Computing – HiPC 2007}, keywords = {cuda, md, software}, pages = {185--196}, posted-at = {2008-03-01 17:35:33}, priority = {4}, title = {Molecular Dynamics Simulations on Commodity GPUs with CUDA}, url = {http://dx.doi.org/10.1007/978-3-540-77220-0\_20}, year = {2007} }

TY - CHAP ID - citeulike:2453098 L3 - citeulike-article-id:2453098 TI - Molecular Dynamics Simulations on Commodity GPUs with CUDA JF - High Performance Computing – HiPC 2007 SP - 185 EP - 196 N2 - 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. KW - cuda KW - md KW - software AU - Liu, Weiguo AU - Schmidt, Bertil AU - Voss, Gerrit AU - Müller-Wittig, Wolfgang PY - 2007/// UR - http://dx.doi.org/10.1007/978-3-540-77220-0_20 ER -