Long timestep molecular dynamics on the graphical processing unit Article

Sweet, JC, Nowling, RJ, Cickovski, T et al. (2013). Long timestep molecular dynamics on the graphical processing unit . Journal of Chemical Theory and Computation, 9(8), 3267-3281. 10.1021/ct400331r

cited authors

  • Sweet, JC; Nowling, RJ; Cickovski, T; Sweet, CR; Pande, VS; Izaguirre, JA

abstract

  • 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 graphical processing unit (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 μs/day using implicit solvent models. © 2013 American Chemical Society.

authors

publication date

  • August 13, 2013

published in

Digital Object Identifier (DOI)

start page

  • 3267

end page

  • 3281

volume

  • 9

issue

  • 8