The Q-cycle mechanism of the bc(1) complex is now well enough understood to allow application of advanced computational approaches to the study of atomistic processes: In addition to the main features of the mechanism, these include control and gating of the bifurcated reaction at the Qo-site, through which generation of damaging reactive oxygen species is minimized:. We report a new molecular dynamics model of the Rhodobacter sphaetoides bc(1) complex implemented in a native membrane, and constructed so as to eliminate blemishes apparent in earlier Rhodobacter models. Unconstrained MD simulations after equilibration with ubiquinol and ubiquinone respectively at Q(o)- and Q-sites show that substrate binding configurations at both sites are different in important details from earlier models. We also demonstrate a new Q(o)-site intermediate, formed in the sub-ms time range, in which semiquinone remains complexed with the reduced iron sulfur protein. We discuss this, and a spring-loaded mechanism for modulating interactions of the iron sulfur protein with occupants of the Q(o)-site, in the context of Control and gating roles. Such atomistic features of the mechanism can usefully be explored through simulation, but we stress the importance of constraints from physical chemistry and biology, both in setting up a simulation and in interpreting results.