Brownian Dynamics of Biological Molecules

The features of Browndye include:

  • Brownian dynamics (BD) simulations on collections of of cores, large rigid bodies composed of many smaller spheres, and chains, flexible assemblies of spheres that can interact with each other and the cores.
  • In addition to outputting trajectories, it can also compute the 2nd-order rate constant of the encounter of two groups, and relative probabilities of transitions from one conformation or binding mode to another.
  • Ability to use user-specified force fields.
  • Complete documentation, including a tutorial for new users.
  • It has functionality very similar to the packages SDA, GeomBD2, and MacroDox.

This software is being developed by Gary Huber in the McCammon Research Group.

If using BrownDye in a publication, please cite the following paper:
G. A. Huber and J. A. McCammon. Browndye: a software package for Brownian dynamics. Computer Physics Communications, 181:1896–1905, 2010.

Browndye 2

Released Dec. 29, 2023

Browndye2 is the new version of the software with several new features, including:

  • Using flexible chains
  • Option to use user-defined force fields
  • Refactoring of various utilities

Browndye 1

Released Feb 13, 2019

Browndye 1 is the original version of the software. It is not being developed any longer.