BD BOX: Difference between revisions
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'''BD_BOX''' | '''BD_BOX''' is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms. | ||
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 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. | 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. | ||
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==References== | ==References== | ||
[http://dx.doi.org/10.1002/jcc.21847 Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734-2744, 2011] | |||
[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013] | |||
[http://pubs.acs.org/doi/pdf/10.1021/ct300937z 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] | |||
[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 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== | ==External links== | ||
*[http://browniandynamics.org BD_BOX Home Page] | *[http://browniandynamics.org BD_BOX Home Page] | ||
[[Category: Materials modelling and computer simulation codes]] | [[Category: Materials modelling and computer simulation codes]] | ||
Revision as of 12:58, 21 October 2014
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.