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Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska
Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Zwirki i Wigury 93, Warsaw 02-089, Poland
Journal of Computational Chemistry, 2011

@article{dlugoszbrownian,

   title={Brownian dynamics simulations on CPU and GPU with BD_BOX},

   author={D{l}ugosz, M. and Zieli{‘n}ski, P. and Trylska, J.},

   journal={Journal of Computational Chemistry},

   publisher={Wiley Online Library},

   year={2011}

}

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Abstract There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU.
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