The supercomputer modeling the processes of creating metal composite materials using the supersonic cold gas-dynamic spraying the nanoclusters on a substrate is considered. The general relevance of the research is related to the development of technology for manufacturing nanoscale interconnections of electrical circuits that supply elements of very large-scale integrated circuits (VLSI). The relevance of this specific study is associated with the need to develop a mathematical apparatus and program tools for modeling all stages of composite creation technology. In this work, the final stage of the process is considered, where individual metal nanoclusters interact with each other and with the substrate. These processes are studied at the atomic-molecular level using molecular dynamics (MD) models. The integration of the MD equations is based on the velocity Verlet scheme using thermo- and barostats. Parallel algorithms are constructed on the basis of spatial decomposition of the computational domain and the methods for dynamic balancing the computing load. The program implementation is focused on the use of MPI and OpenMP technologies. The novelty of this study is associated with the development of a new approach to the calculations of different-material metallic systems based on applying the embedded atom model potential. As an example, the problem of copper and nickel nanoclusters interaction during the manufacture of the corresponding nanocomposite is chosen. Such nanocomposite is often used as an interconnection for elements of modern VLSI. Obtained results confirm the correctness of the developed computational procedure and the possibility of supercomputer modeling of metal composite nanostructures.