Computer modeling of plastic deformation of f.c.c.-metal (Al, Cu, Pt) nanocrystals is performed by the molecular dynamics method using the new techniques for high-performance computing on the basis of ‘scientific gateway’ (Science Gateway) and WS-PGRADE/gUSE technologies, ‘service grid’ and ‘desktop grid’ infrastructures. The new features of evolution are revealed for irregular atomic arrangements (i.e. so-called atom—vacancy states), which arise in process of monotonic uniaxial load of nanocrystals in cubic orientation. As shown, the collective restructuring in the ensemble of atom—vacancy states leads to significant changes of the average stress values. As a result of the evolution, the collective self-organized zones of strain localization appear as quasi-periodic bands with various quantitative parameters for different metals (thickness, period, time of formation), but with the same qualitative characteristics (non-crystallographic orientation, evolution, slope, through-bulk arrangement, outcropping). The simulated bands with nonuniform stress distribution are treated as precursors of the correlated movement of groups of atom—vacancy (or highly excited) states, i.e., precursors of inhomogeneous localized (hydrodynamic) plastic flow in channels at low (nanometre) scale level. With the further evolution, these bands may be the carriers of the hydrodynamic deformation modes at the micro- and macroscale levels, which have been observed in the experiments by various research groups. The simulation of results of X-ray analysis shows that the diffraction peaks decrease and shift with increase of plastic strain that indicates the presence of point defects. Thus, in a qualitative sense, we can conclude that the interpretation of the irregular atomic arrangements in this work as the point defects with the properties of the atom—vacancy states is correct. On the basis of these results and their discussion, it is concluded that plastic deformation of nanocrystals of f.c.c. metals under conditions, when dislocation slip is impossible, is realized by the localized hydrodynamic flow of matter in channels with loosely packed noncrystalline (liquid-like) structure by means of generation of metastable point defects of atom—vacancy type, their evolution and self-organization in the localized bands at the larger scales.