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.
Keywords for this software
References in zbMATH (referenced in 3 articles )
Showing results 1 to 3 of 3.
- Jiang, Shidong; Liang, Zhi; Huang, Jingfang: A fast algorithm for Brownian dynamics simulation with hydrodynamic interactions (2013)
- Zhang, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai: A Fourier-series-based kernel-independent fast multipole method (2011)
- Huber, Gary A.; McCammon, J. Andrew: Browndye: A software package for Brownian dynamics (2010)