title: Brownian dynamics simulations on CPU and GPU with BD_BOX.
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.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland. mdlugosz@icm.edu.pl
authors.forename: Maciej
authors.initials: M
authors.lastname: Długosz
authors.forename: Paweł
authors.initials: P
authors.lastname: Zieliński
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D003198:Computer Simulation; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D012984:Software