We report potential of mean force calculations based on molecular dynamics simulations of the stacking-unstacking process of the ribodinucleoside monophosphate adenylyl-3’,5’-adenosine (ApA). In the simulations of the stacking-unstacking process of ApA we used a complete all atom treatment, which included effects from the sugar phosphate backbone and the aqueous solution. The fluctuations of the torsion angles were observed to be larger with increased temperature. We show here that the stacking-unstacking process of ApA is very temperature dependent and that the barrier of going from a stacked state to an unstacked becomes smaller at higher temperatures. Thermodynamic parameters as entropy and enthalpy were obtained by performing these potential of mean force calculations at different temperatures and good agreement with experimental data were found.