GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis

Ivan Teo, Juan Perilla, Rezvan Shahoei, Ryan McGreevy, Chris Harrison
University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology, NIH Resource for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign, 2014


   title={GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis},

   author={Teo, Ivan and Perilla, Juan and Shahoei, Rezvan and McGreevy, Ryan and Harrison, Chris},



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This tutorial will demonstrate how to use features in NAMD and VMD to harness the computational power of graphics processing units (GPUs) to accelerate simulation, visualization and analysis. You will learn how to drastically improve the efficiency of your computational work, achieving large speedups over CPU only methods. You will explore ways of investigating large multimillion atom systems or long simulation timescales through easy to use features of NAMD and VMD on readily available hardware. Please note that completeing the tutorial examples will require a computer with a CUDA-capable NVIDIA GPU.
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