ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units.

@article{Biedermann2015ReaDDyMMFI,
  title={ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units.},
  author={Johann Biedermann and Alexander Ullrich and Johannes Sch{\"o}neberg and Frank No{\'e}},
  journal={Biophysical journal},
  year={2015},
  volume={108 3},
  pages={457-61}
}
ReaDDy is a modular particle simulation package combining off-lattice reaction kinetics with arbitrary particle interaction forces. Here we present a graphical processing unit implementation of ReaDDy that employs the fast multiplatform molecular dynamics package OpenMM. A speedup of up to two orders of magnitude is demonstrated, giving us access to… CONTINUE READING