Programs in Physics & Physical Chemistry
|[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.|
External routines: uses the output of APBS  (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.
Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces.
Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.
|||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.|
|Disclaimer | ScienceDirect | CPC Journal | CPC | QUB|