BD BOX

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. Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system. 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

Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734-2744, 2011

Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013

Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014

Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014

External links

• BD_BOX Home Page