BD BOX
BD_BOX program [1]
BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.
Work on BD_BOX is supported by Polish National Science Centre.
References
- ↑ [http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011