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Herein, the molecular dynamics (MD) simulations of pure Ni crystallites are performed to show the influence of the grain boundary (GB) geometry on the values of the activation energy of GB migration. The considered systems are bicrystal with Σ5[010] tilt plane boundary, spherical grain with initial curvature radius 5 nm, and polycrystalline 30 nm × 30 nm × 30 nm block. The motion of three types of GBs (flat, spherical, and polycrystalline) at constant temperatures and no applied forces is studied. The obtained values of activation energy are 0.45, 0.11, and 0.57 eV for flat, spherical, and polycrystalline types of GBs, respectively. These values are smaller than those that are reported in experimental works, which is a common issue for atomistic simulations of GB migration. Possible sources of such disagreement and ways to overcome it are discussed. The particular part of this work is devoted to the development of the automated analysis of polycrystalline structure. This analysis provides detailed information on grain size distribution and its evolution in time.