To compute the association rate constant (kon) for receptorligand complexes, we must use BD. BD simulations are computationally less expensive as compared to MD simulations due to implicit solvent and approximations such as the often-used rigid body approximation. Moreover, the encounter-based approach focuses on the initial stages of the binding process when the ligand is far from the receptor-binding site, and the approximations in BD suffice as a physical description. Explicit electrostatic interactions are considered between the protein and the ligand, which is particularly important for receptor-ligand complexes where electrostatic forces play a significant role in molecular recognition and binding. Browndye is a software package that runs the BD simulations to compute the second-order rate constants for encountering two molecules using a simplified physical model. Brownian dynamics describes motion at a mesoscopic level, in which models of large molecules are usually simplified to smaller collections of rigid bodies, and the solvent is treated using continuum theories instead of explicitly with individual molecules. A recent review summarizes theoretical details, common methods and software, and some of the most recent applications of BD . Considering Newton's equations of motion and assuming a separation between the time scales of the macromolecules and the solvent molecules, one can derive the following stochastic differential equation of motion :