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'''BD_BOX''' | '''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> <ref>Work on BD_BOX is supported by the [https://www.ncn.gov.pl/ Polish National Science Centre]</ref> 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 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-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. | ||
==References== | ==References== | ||
<references/> | |||
;Related reading | |||
[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz | *[http://pubs.acs.org/doi/abs/10.1021/ct500124r Maciej Długosz and Jan M. Antosiewicz "Anisotropic diffusion effects on the barnase-barstar encounter kinetics" Journal of Chemical Theory and Computation '''9''' pp. 1667-1677 (2013)] | ||
*[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 Długosz | *[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 Długosz | |||
==External links== | ==External links== | ||
*[http://www3.cent.uw.edu.pl/~mdlugosz BD_BOX Home Page] | *[http://www3.cent.uw.edu.pl/~mdlugosz/#download BD_BOX Home Page] | ||
[[Category: Materials modelling and computer simulation codes]] | [[Category: Materials modelling and computer simulation codes]] | ||
Latest revision as of 13:28, 6 July 2016
BD_BOX [1] [2] 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.
References[edit]
- Related reading
- Maciej Długosz and Jan M. Antosiewicz "Anisotropic diffusion effects on the barnase-barstar encounter kinetics" Journal of Chemical Theory and Computation 9 pp. 1667-1677 (2013)
- 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)
- 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)