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GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten
Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave., Urbana, IL 61801, United States
Journal of Molecular Graphics and Modelling, Vol. 29, No. 2. (08 September 2010), pp. 116-125

@article{stone2010gpu,

   title={GPU-accelerated molecular modeling coming of age},

   author={Stone, J.E. and Hardy, D.J. and Ufimtsev, I.S. and Schulten, K.},

   journal={Journal of Molecular Graphics and Modelling},

   issn={1093-3263},

   year={2010},

   publisher={Elsevier}

}

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Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude speedup over CPU code and in special cases providing speedups of two orders of magnitude. This paper surveys the development of molecular modeling algorithms that leverage GPU computing, the advances already made and remaining issues to be resolved, and the continuing evolution of GPU technology that promises to become even more useful to molecular modeling. Hardware acceleration with commodity GPUs is expected to benefit the overall computational biology community by bringing teraflops performance to desktop workstations and in some cases potentially changing what were formerly batch-mode computational jobs into interactive tasks.
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