Browndye: A software package for Brownian dynamics

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems.Program summaryProgram title: BrowndyeCatalogue identifier: AEGT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: MIT license, included in distributionNo. of lines in distributed program, including test data, etc.: 143 618No. of bytes in distributed program, including test data, etc.: 1 067 861Distribution format: tar.gzProgramming language: C++, OCaml (http://caml.inria.fr/)Computer: PC, Workstation, ClusterOperating system: LinuxHas the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreadsRAM: Depends linearly on size of physical systemClassification: 3External 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. USA 98 (18) (2001) 10037–10041.