The interaction of supercritical turbulent flows with granular sediment beds is challenging to study both experimentally and numerically. This challenging task has hampered advances in understanding antidunes, the most characteristic bedform of supercritical flows. This article presents the first numerical attempt to simulate upstream-migrating antidunes with geometrically resolved particles and a liquid-gas interface. Our simulations provide data at a resolution higher than laboratory experiments, and they can therefore provide new insights into the mechanisms of antidune migration and contribute to a deeper understanding of the underlying physics. To manage the simulations' computational costs and physical complexity, we employ the cumulant lattice Boltzmann method in conjunction with a discrete element method for particle interactions, as well as a volume-of-fluid scheme to track the deformable free surface of the fluid. By reproducing two flow configurations of previous experiments (Pascal et al., Earth Surf. Process. Landf., vol. 46, issue 9, 2021, pp. 1750-1765), we demonstrate that our approach is robust and accurately predicts the antidunes' amplitude, wavelength and celerity. Furthermore, the simulated wall shear stress, a key parameter governing sediment transport, is in excellent agreement with the experimental measurements. The highly resolved data of fluid and particle motion from our simulation approach open new perspectives for detailed studies of morphodynamics in shallow supercritical flows.