Brownian Dynamics Simulations on CPU and GPU with BD_BOX

Maciej Długosz , Paweł Zieliński , Joanna Trylska

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.
Author Maciej Długosz
Maciej Długosz,,
-
, Paweł Zieliński ISE
Paweł Zieliński,,
- The Institute of Electronic Systems
, Joanna Trylska
Joanna Trylska,,
-
Journal seriesJournal of Computational Chemistry, ISSN 1096-987X
Issue year2011
Vol32
No12
Pages2734-2744
Keywords in EnglishBrownian dynamics; hydrodynamic interactions; scalability; MPI; OpenMP; CUDA
DOIDOI:10.1002/jcc.21847
URL http://onlinelibrary.wiley.com/doi/10.1002/jcc.21847/pdf
Languageen angielski
Score (nominal)40
Publication indicators WoS Impact Factor: 2011 = 4.583 (2) - 2011=4.795 (5)
Citation count*0 (2015-03-16)
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