The effective fragment potential (EFP) method is an efficient ab initio based polarizable model that describes the explicit solvent effects, is applied to glycine dipeptide solvated in water. The structures of neutral and zwitterionic glycine dipeptide immersed in water layers of 5.0 and 6.0 Å are investigated by performing RHF/EFP geometry optimizations at the RHF/cc-pVDZ level of theory. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order Møller– Plesset theory (MP2)/cc-pVDZ level.