A confinement model of finite-size systems that embodies an equation of state is presented. The temperature and pressure of the system are obtained from the positions and velocities of the enclosed particles after a number of molecular dynamics simulations. The pressure has static and dynamic (thermal) contributions, extending the Mie-Gruneisen equation of state to include weakly interacting anharmonic oscillators. The model is applied to a system of 13 H-2 molecules under low-pressure and low-temperature conditions in the classical regime. The confining cage in this case is a spherical hydrogen cavity. The Born-Oppenheimer molecular dynamics in conjunction with density functional theory are used for the time evolution of the particle system. The hydrogen molecules form a noncrystalline cluster structure with icosahedral symmetry that remains so in the whole temperature range investigated. The fluctuations of the interatomic distances increase with the temperature, while the orientational order of the enclosed system of molecules fades out, suggesting a gradual order-disorder transition.