Browndye: A software package for Brownian dynamics

  title={Browndye: A software package for Brownian dynamics},
  author={Gary A. Huber and James Andrew McCammon},
  journal={Computer physics communications},
  volume={181 11},
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. 

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Molecular Biology of the Cell

  • B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter
  • 4th edition, Garland Science, New York
  • 2002
Highly Influential
10 Excerpts

Using expat

  • C. Cooper
  • 1999
Highly Influential
2 Excerpts

Diffusive reaction-rates from Brownian dynamics simulations – replacing the outer cutoff surface by an analytical treatment

  • B. Luty, J. McCammon, H. Zhou
  • J. Chem. Phys. 97 (8)
  • 1992
Highly Influential
3 Excerpts

Posix threads programming

  • B. Barney
  • pthreads/
  • 2009
1 Excerpt


  • X. Leroy, D. Doligez, J. Garrigue, D. Rémy
  • Vouillon, The objective Caml system: release 3.11…
  • 2008

Cell Biology

  • T. Pollard, W. Earnshaw
  • W.B. Saunders, New York
  • 2007
1 Excerpt

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