Gordon, DanielHoyles, MatthewChung, Shin-Ho2015-12-071539-3755http://hdl.handle.net/1885/25481We present an algorithm for performing rigid-body Brownian dynamics that can take into account the hydrodynamic properties (translational and rotational friction tensors and the coupling between them) of each rigid body. In the zero temperature limit, the error term scales as Δ4 for time step Δ, while at nonzero temperatures the error scaling is Δ5/2. We test the algorithm by applying it to a molecule of four-aminopyridine in water. We intend to use the algorithm to model the interaction between biological ion channels and other channel blocker molecules, but it may also have applicability to modeling other small particles such as colloids or nanoparticles.Keywords: Aminopyridines; Biological ion channels; Brownian Dynamics; Channel blockers; Error terms; Hydrodynamic properties; Nonzero temperature; Rigid body; Rotational friction; Small particles; Time step; Zero temperatures; Brownian movement; Algorithms200910.1103/PhysRevE.80.0667032016-02-24