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Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN
University of Notre Dame, 2012

@article{sweet2012long,

   title={Long Timestep Molecular Dynamics on the Graphical Processing Unit},

   author={Sweet, J.C. and Nowling, R.J. and Cickovski, T. and Sweet, C.R. and Pande, V.S. and Izaguirre, J.A.},

   year={2012}

}

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Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 ms/day using implicit solvent models.
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