The mechanism of eutectic formation was investigated via computer-aided molecular dynamics techniques based on experimental results. The CBZ group mixtures CBZ-L-Asp/D-AlaNH(2)center dot HCl/methanol, CBZ-L-Asp/L-PheOMe center dot HCl/methanol, and CBZ-L-Tyr/L-ArgNH(2)center dot 2HCl/methanol formed transparent eutectic melts. The non-CBZ group mixtures L-Asp/D-AlaNH(2)center dot HCl/methanol, L-Asp/L-PheOMe center dot HCl/methanol, and L-Tyr/L-ArgNH(2)center dot 2HCl/methanol did not form eutectic melts. According to molecular dynamics simulation results, increase in the kinetic energy values of eutectic forming mixtures was much larger than the increase in potential energy over a temperature shift from 298 to 333 K. However, the results for non-eutectic forming mixtures were reversed. The Coulomb interaction energies of eutectic forming mixtures significantly decreased, because eutectic melting can increase the mobility of molecules in the mixtures. The enhancement of molecular mobility was confirmed by increased self-diffusion constant values, and the change of solid-to-liquid phase was detected by radial distribution function results. The periodic boundary conditions for calculation of molecular dynamics were found to be reliable.