An analytical potential function of the glycine-water system, which can describe not only a reactive potential energy surface but also the interaction energy with water, has been proposed, by the empirical valence bond method with the exchange matrix element improved by Chang and Miller to reproduce an ab initio molecular orbital (MO) surface with high accuracy. The fitted potential function can reproduce satisfactorily the Born-Oppenheimer adiabatic surface obtained by ab initio MO calculations. Further, by molecular dynamics (MD) simulation and the free energy perturbation theory, we have presented the average of the interaction energy of glycine with water and the flee energy profile of its intramolecular proton transfer reaction along the intrinsic reaction coordinate. It has been found that the zwitterionic form of glycine is much more stable than the neutral form, which is consistent with the result of Clementi et al. We obtained the free energy change of the reaction and that of activation to be 8.46 and 16.85, kcal/mol, respectively, which are in good agreement with the experimental values. We conclude that our potential function can work very well for the MD simulations of the chemical reaction.