Premium
Brownian dynamics simulations on CPU and GPU with BD_BOX
Author(s) -
Długosz Maciej,
Zieliński Paweł,
Trylska Joanna
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21847
Subject(s) - computer science , cuda , parallel computing , computational science , software , brownian dynamics , general purpose computing on graphics processing units , supercomputer , molecular dynamics , brownian motion , computer graphics (images) , physics , chemistry , computational chemistry , graphics , operating system , quantum mechanics
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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011