Molecular dynamics (MD) simulations were performed for a Zr2Ni alloy by referring to crystallographic features of a metastable Zr2Ni phase. Simulation method was identical to our previous studies named plastic crystal model (PCM), which includes crystallographic operations for an intermetallic compound in terms of the random rotations of hypothetical clusters around their center of gravity and subsequent annealing at a low temperature. On the basis of MD-PCM, the present study considers an additional refinement named united atom scheme (UAS) on the motions of atoms in the hypothetical clusters. In MD-PCM-UAS, Dreiding potential was assigned for atomic bonds in a cluster whereas Generalized Embedded Atom Method potential for the other atomic pairs. The simulation results by MD-PCM-UAS yield a liquid-like structure. However, annealing did not cause subsequent structural relaxation, which differs from the results by MD-PCM and conventional MD simulations. Further simulations based on MD-PCM-UAS were performed for a nanostructure comprising clusters and glue atoms, leading to the best fit with the experimental data.