The purpose of this study is to obtain the heat transfer phenomena of bio-tissue by the external heating. The molecular dynamics (MD)algorithm and the GROMACS protein data bank are used to analyze the bio-heat transfer
characteristics of Alanine molecules in the micro-scale. The simulations focus specifically on the temperature evolution and thermal conductivity of the Alanine molecules under different kinds of thermal boundary conditions.The thermal conductivity of the Alanine molecule is calculated via the autocorrelation function of the Green-Kubo formalism. Overall, the results presented in this study provide a useful source of reference for improving the efficacy of thermal ablation and the phenomena of the micro-scale hyperthermia.