Solvent Effect on Conformational Stability in the Ala Dipeptide: Full Free Energy Simulations Abstract: We report herein theoretical studies of the ocnformational stability of the Ala dipeptide as an isolated molecule in water. The C₇, C₅, a_R and P_II conformational forms are considered. The thermodynamics of hydration were computed by liquid state computer simulation on a solute and 202 water molecules under periodic boundary conditions at T=25^oC. The free energy of hydration was computed by determining the relative probabilities of conformations that lie on a line between conformatiosn in the (y,f) space. The intramolecular thermodynamics was worked out by Monte Carlo methods in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of atomic displacements. The total free energy, intramolecular plus hydration, is found to be similar for C₇, a_R and P_II, and thus it is reasonable to expect that all forms are thermally populated at room temperature.