Structure-H hydrate is the crystalline compounds in which the water molecules form a cavity enclosing guest molecule and the other guest molecule, which is called LMGS. The stability of structure-H hydrate is strongly dependent on LMGS. Structure-H hydrate is thought to be the new means of storage and transportation of natural gas. The stability of hydrate should be clarified. In this study, Molecular dynamics (MD) simulation has been carried out so as to investigate the stability of structure-H hydrate. The stability of structure-H hydrate is evaluated by Free energy difference, which is calculated directly by MD simulation. LMGS is treated as Lennard-Jones one site model so as to compare the free energy difference easily. The free energy of structure-H is minimized when a of LMGS is about 6〓, while it becomes lower as ε is increased. All simulation is performed on special purpose computer, MDGRAPE-2.