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[Licence| Download | New Version Template] aegt_v1_0.tar.gz(1042 Kbytes)
Manuscript Title: Browndye: A Software Package for Brownian Dynamics
Authors: Gary A. Huber, J. Andrew McCammon
Program title: Browndye
Catalogue identifier: AEGT_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 181(2010)1896
Programming language: C++, OCaml (http://caml.inria.fr/).
Computer: PC, Workstation, Cluster.
Operating system: Linux.
Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads
RAM: Depends linearly on size of physical system
Keywords: Brownian dynamics, protein association, software, diffusion, kinetics.
Classification: 3.

External routines: uses the output of APBS [1] (http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately.
Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution.

Nature of problem:
Exploration and determination of rate constants of bimolecular interactions involving large biological molecules.

Solution method:
Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces.

Running time:
Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

References:
[1] N. Baker, D. Sept, S. Joseph, M. Holst, J. McCammon, Electrostatics of nanosystems: Application to microtubules and the ribosome, Proc. Natl. Acad. Sci. U. S. A. 98 (18) (2001) 10037-10041.