A major challenge in simulating glassy systems is the ability to generate configurations that may be found in equilibrium at sufficiently low temperatures, in order to probe static and dynamic behavior close to the glass transition. A variety of approaches have recently explored ways of surmounting this obstacle. Here, we explore the possibility of employing mechanical agitation, in the form of cyclic shear deformation, to generate low energy configurations in a model glass former. We perform shear deformation simulations over a range of temperatures, shear rates, and strain amplitudes. We find that shear deformation induces faster relaxation toward low energy configurations, or overaging, in simulations at sufficiently low temperatures, consistently with previous results for athermal shear. However, for temperatures at which simulations can be run until a steady state is reached with or without shear deformation, we find that the inclusion of shear deformation does not result in any speed up of the relaxation toward low energy configurations. Although we find the configurations from shear simulations to have properties indistinguishable from an equilibrium ensemble, the cyclic shear procedure does not guarantee that we generate an equilibrium ensemble at a desired temperature. In order to ensure equilibrium sampling, we develop a hybrid Monte Carlo algorithm that employs cyclic shear as a trial generation step and has acceptance probabilities that depend not only on the change in internal energy but also on the heat dissipated (equivalently, work done). We show that such an algorithm, indeed, generates an equilibrium ensemble.