The paper is organized as follows. In Section II, we present the theory and illustrate the numerical procedures employed to determine the effective modes in alanine (Section II A) and to generate the MD trajectory (Section II B). Section III is devoted to a detailed presentation of the results: in Section III A, the neutral and zwitterionic forms of alanine are compared in the gas phase; in Section III B, the hydrated and crystalline zwitterionic forms are studied. Our conclusions are presented in Section IV.