•The convention void method has been improved.•Nonequilibrium thermodynamic integration method displays the highest accuracy for melting temperature.•The melting temperature of Ni-Zr compound system were investigated with five different methods. Finding the efficient and accurate schemes to calculate the melting temperature is important for molecular dynamics simulation. We propose a modified void method based on heterogeneous nucleation to validly calculate the melting temperature from solid-liquid coexistence state. It decreases the degree of superheating in the conventional voids method. The efficiency and accuracy of five methods (i.e., hysteresis method, two phase coexistence method, the interface pinning method, the Frenkel-Ladd path method and the modified void method) have been discussed in detail. The calculated results of hysteresis method strongly depend on heating/cooling rate. For the nonequilibrium thermodynamic integration method, the calculated accuracy is consistent with the interface pinning method for monoatomic Cu. For the modified void method the calculated results agree with the nonequilibrium thermodynamic integration method.