Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz
Computer Science and Engg., University at Buffalo, Buffalo, NY 14260


   title={Accelerating Molecular Dynamics Simulations with GPUs},

   author={Walters, J.P. and Balu, V. and Chaudhary, V. and Kofke, D. and Schultz, A.}


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Molecular dynamics simulations are known to run for many days or weeks before completion. In this paper we explore the use of GPUs to accelerate a Lennard-Jones-based molecular dynamics simulation of up to 27000 atoms. We demonstrate speedups that exceed 100x on commodity Nvidia GPUs and discuss the strategies that allow for such exceptional speedups. We show that traditional molecular dynamics simulations can be greatly improved from a runtime of over 1 day to 18 minutes.
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