Brownian Dynamics Simulations on CPU and GPU with BD_BOX
Maciej Długosz , Paweł Zieliński , Joanna Trylska
AbstractThere 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.
|Journal series||Journal of Computational Chemistry, ISSN 1096-987X, (A 40 pkt)|
|Keywords in English||Brownian dynamics; hydrodynamic interactions; scalability; MPI; OpenMP; CUDA|
|Publication indicators||: 2011 = 4.583 (2) - 2011=4.795 (5)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.