1. A molecular simulation method that acquires physical properties or physical quantities of a predetermined shape using simulation, the molecular simulation method comprising: arranging atoms in the predetermined shape; acquiring interatomic potential based on the positions of the arranged atoms and an interatomic bond energy determined based on a Young's modulus; and carrying out a molecular dynamics calculation based on the acquired interatomic potential, and acquiring the physical properties or the physical quantities, wherein when acquiring interatomic potential based on the positions of the arranged atoms, there are acquired potential parameters including the interatomic bond energy of the two of the atoms based on a cross-sectional area on which the two of the atoms act between Voronoi points obtained by a Voronoi polyhedron analysis using points of the atoms arranged by the atom arranging part, and the interatomic potential is determined using the acquired potential parameters.