## Browndye

swMATH ID: | 8086 |

Software Authors: | Huber, Gary A.; McCammon, J.Andrew |

Description: | 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. |

Homepage: | http://browndye.ucsd.edu/ |

Related Software: | Matlab; Fastcap; AFMPB; VMD; SDA; UHBD; Macrodox; OCaml; APBS |

Referenced in: | 3 Publications |

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### Referenced by 8 Authors

2 | Huang, Jingfang |

1 | Huber, Gary A. |

1 | Jiang, Shidong |

1 | Liang, Zhi |

1 | McCammon, J. Andrew |

1 | Pitsianis, Nikos P. |

1 | Sun, Xiaobai |

1 | Zhang, Bo |

### Referenced in 3 Serials

1 | Computer Physics Communications |

1 | Journal of Computational Physics |

1 | Mathematics of Computation |

### Referenced in 4 Fields

2 | Numerical analysis (65-XX) |

1 | Harmonic analysis on Euclidean spaces (42-XX) |

1 | Fluid mechanics (76-XX) |

1 | Biology and other natural sciences (92-XX) |