Molecular dynamics simulation is carried out for the bubble nucleation of water and liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. When heat is added into the molecular cluster, liquid initial equilibrium temperature and molecular cluster size can affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of the bubble nucleation, the potential energy of the system slowly increases. In the process of bubble nucleation of explosive boiling, the lower initial equilibrium temperature leads to the bigger size of the molecular cluster. With more heat added into the system of the simulation cell, the potential energy varies in a larger range. The primary potential of water molecules includes Lennard-Jones potential energy and Columbic force caused by static charges of oxygen and hydrogen atoms. This is the reason why the bubble nucleation of water is different from that of liquid nitrogen. Pressure controlling is applied in the simulation of water, which makes the bubble more fully extended than that of liquid nitrogen.