Electrostatics and diffusion of molecules in solution – simulations with the University-of-Houston Brownian dynamics program. This paper is a follow-up to the initial communication (Comput. Phys. Commun. 62 (1991) 187–197) on the Brownian Dynamics/Electrostatics program UHBD developed at the University of Houston. The program is now capable of computing pKas of ionizable groups in proteins, performing Brownian dynamics simulations with a flexible substrate and target, and molecular mechanics/dynamics calculations using a continuum solvent. These new capabilities and other features are discussed along with selected applications which illustrate the capabilities of the current version of UHBD.