We report results of simulations of the association process between the p-sulfonatocalix[4]arene and the ammonium cation. We have calculated the free energy profile of the calixarene-ammonium system in water as a function of the separation distance using the FEP formalism. The potential of mean force (PMF) profile and the MD simulations of the endpoints of this PMF curve show that the ammonium cation is not complexed by the calixarene. In addition, we have studied the complexes of the calixarene with methylammonium, tetramethylammonium and tetraethylammonium cations in water. We have shown the insertion of the tetraalkylammonium cations into the cavity of the calixarene by calculating the number of alkyl groups inside the cavity. A correlation between the number of inserted alkyl groups and the experimental enthalpy of complexation has been found. We have shown that, at the structural and energetic levels, the United Atom (UA) and All Atom (AA) descriptions give similar results for the tetramethylammonium complex. The influence of the pH on the structure and energetics of the tetramethylammonium and tetraethyl ammonium complexes has also been examined.