Geodesic
Parallel molecular dynamics with Ewald summation and integration on GPU
Numerical methods and programming, Tome 10 (2009) no. 2, pp. 158-175

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The problem of molecular dynamics simulation with periodic boundary conditions is considered. Efficient algorithms for the Ewald summation method are discussed. Parallel implementations on GPU with NVIDIA CUDA technology are proposed. The integration of motion equations on GPU with single and double precision of floating point arithmetic is analyzed. On an NVIDIA GeForce GTX 280 video card, a remarkable speed-up up to 890 times is achieved compared to a scalar code running on Intel Core 2 Quad Q9550 CPU.
Keywords: molecular dynamics; Ewald summation; parallel computing; graphics processors; CUDA. 
@article{VMP_2009_10_2_a0,
     author = {A. S. Boyarchenkov and S. I. Potashnikov},
     title = {Parallel molecular dynamics with {Ewald} summation and integration on {GPU}},
     journal = {Numerical methods and programming},
     pages = {158--175},
     publisher = {mathdoc},
     volume = {10},
     number = {2},
     year = {2009},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/VMP_2009_10_2_a0/}
}
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A. S. Boyarchenkov; S. I. Potashnikov. Parallel molecular dynamics with Ewald summation and integration on GPU. Numerical methods and programming, Tome 10 (2009) no. 2, pp. 158-175. http://geodesic.mathdoc.fr/item/VMP_2009_10_2_a0/