This study develops a hybrid numerical scheme based on a molecular dynamics (MD) algorithm and the GROMACS protein data bank to analyze the thermal bio-flow of alanine molecules in a microchannel. The numerical results show that the velocity profiles in the microchannel are highly dependent on both global effects, i.e. the effective channel width and local effects, i.e. the thermal boundary conditions. Specifically, the magnitude of the fluctuations observed in the velocity profiles increase as the channel width decreases or as the thermal boundary temperature increases. The results presented in this study provide useful information regarding suitable microchannel widths and operational temperatures for bio-chip devices and contribute a further understanding of basic human thermal bio-flow phenomena, particularly, regarding the correlation between the rate of local metabolism, burn and frostbite events, respectively.