The presence of stable facets of nanobubbles in crystal lattice can significantly affect their diffusion coefficient, but the existing theory of this phenomenon is too general and can not take into account atomistic structure of nanobubbles in a given material. Such a theory for the mechanisms of bubble motion in crystals can be extended and developed using methods of atomistic modelling. In this work, we consider the movement of bubbles in the bcc lattice of γ-U. The Beere’s theory of faceted bubble motion is revised and a method of non-equilibrium accelerated molecular dynamics in a pressure gradient is proposed. The results of the accelerated method calculations for γ-U are verified using generic molecular-dynamics calculations of free nanobubble diffusion. The new method significantly accelerates calculations of the diffusion coefficient for nanometer-sized bubbles and opens the way for more accurate material-specific calculations of gas-filled nanobubbles diffusivity in nuclear fuels.