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'''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Pawel Zieliński and Joanna Trylska "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734-2744 (2011) | '''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Pawel Zieliński and Joanna Trylska "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734-2744 (2011)]</ref> is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms. | ||
BD_BOX uses [[Flexible molecules |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 model |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 boundary conditions |periodic]] multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. | BD_BOX uses [[Flexible molecules |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 model |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 boundary conditions |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 graining |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. | 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 graining |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. | 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== | ==References== | ||
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*[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Maciej Długosz and Jan M. Antosiewicz "Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules Journal of Chemical Theory and Computation '''10''' pp. 2583-290 (2014)] | *[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Maciej Długosz and Jan M. Antosiewicz "Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules Journal of Chemical Theory and Computation '''10''' pp. 2583-290 (2014)] | ||
*[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Maciej Długosz and Jan M. Antosiewicz "Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments" Journal of Chemical Theory and Computation '''10''' pp. 481-491 (2014)] | *[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Maciej Długosz and Jan M. Antosiewicz "Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments" Journal of Chemical Theory and Computation '''10''' pp. 481-491 (2014)] | ||
==External links== | ==External links== | ||