In this paper, the authors present the results of modeling the movement of three methane molecules into a closed carbon nanotube. The main approach in this work is to model the interaction between methane molecules and the structure of a nanocapsule, which is a single-walled closed carbon nanotube. Descriptively, the interaction is represented using molecular dynamics approaches and the Lennard-Jones potential. Methane molecules in this model are material points corresponding to the centers of mass of the molecules. To solve the resulting equations of motion of molecules inside the nanotube, the Runge-Kutta method of the 4th order of accuracy is used. The results obtained are presented in the form of graphs depicting the trajectories of the movement of molecules inside the nanotube as a function of time, graphs of the dependence of the velocities of molecules on time and coordinates, and graphs of the change in the total energy of the system as a function of time. Due to the fact that this model does not implement the energy exchange between the nanostructure and molecules, the total energy must be conserved with some accuracy associated with the computational method. Analyzing the obtained results, it is possible to evaluate the potential possibility of using single-walled closed carbon nanotubes as nanocontainers for transporting or storing methane.