Browndye

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.