Browndye: A software package for Brownian dynamics

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract 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. Title of program: Browndye Catalogue Id: AEGT_v1_0 Nature of problem Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Versions of this program held in the CPC repository in Mendeley Data AEGT_v1_0; Browndye; 10.1016/j.cpc.2010.07.022