Accelerating Molecular Dynamics Simulations with GPUs
John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David A. Kofke, Andrew J. Schultz · 2008
Molecular dynamics simulations are known to run for many days or weeks before completion. In this pa-per 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 com-modity 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. 1