Software News and Updates Brownian Dynamics Simulations on CPU and GPU with BD_BOX
Software News and Updates Brownian Dynamics Simulations on CPU and GPU with BD_BOX
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DOI：
10.1002/jcc.21847
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发表时间：
2011-09-01
影响因子：
3
通讯作者：
Trylska, Joanna
中科院分区：
文献类型：
--
作者：
Dlugosz, Maciej;Zielinski, Pawel;Trylska, Joanna
近年来，由于在拥挤环境中研究单粒子行为的实验技术的发展，人们对在体内条件下模拟生物过程的兴趣越来越大。我们已经开发了一个软件包，BD_BOX，多尺度布朗动力学模拟。BD_BOX可以使用灵活的粗粒度珠模型模拟单分子或多种相互作用分子种类的多组分系统。BD_BOX是用C语言编写的，并采用了现代计算机架构和技术;其中包括用于分布式内存架构的MPI，用于共享内存平台的OpenMP，用于GPGPU的NVIDIA CUDA框架以及用于CPU的SSE矢量化。(C)2011 Wiley Periodicals，Inc. J Comput Chem 32：2734-2744，2011
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. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2734-2744, 2011