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Ni nanoparticle on a graphene substrate, inside the fullerene and carbon nanotube was studied by molecular dynamics simulation technique. Morse interatomic potential have been used for Ni-Ni and Ni-C interactions, and AIREBO potential has been used for CC interaction. The pairwise Morse potential was chosen for the description of the Ni-C interaction because of its simplicity. It is shown that Morse potential can satisfactory reproduce the properties of graphene-nickel system. The effect of boundary conditions on the interaction of Ni nanoparticle and graphene sheet are investigated. It is shown, that if the edges of graphene plane are set to be free, coverage of Ni nanoparticle by graphene or just crumpling of graphene is observed depending on the size of nanoparticle. It is found, that Ni nanoparticle tend to attach to the carbon surface-graphene plane or the shell of fullerene and nanotube. Moreover, Ni nanoparticle induce the deformation of the surface of carbon polymorph. The obtained results are potentially important for understanding of the fabrication of metal-carbon composites and interaction between graphene and metal nanoparticles in such a system.