We report results of simulations of association between p-sulfonatocalix[4]arene and inorganic (rare-earth metal cations) and organic cations (a series of quaternary ammonium cations) in aqueous solution. Our main goals were to obtain structural features for these complexes in aqueous solution and to study the role of water on the cation binding by the p-sulfonatocalix[4]arene. The MID calculations show that the organic and inorganic cations bind in very different modes. The lanthanide cations are located outside the cavity of the calixarene forming an outer-sphere complex, while for the organic cations, the quaternary ammonium cation is included into the cavity of the calixarene. In fact, the Me4N+ cation penetrates deeply into the cavity. As concerns the Et4N+ cation, one of the alkyl chain is close to the center of mass of the calixarene, whereas two other alkyl chains are located near the border of the cavity. In the case of Pr4N+ cation, only one propyl chain is inside the cavity, while the others are outside the cavity of the calixarene. Additional simulations have been carried out using two different free energy perturbation formalisms to calculate differences in Gibbs free energies of complexation of lanthanide complexes. These simulations are consistent with the thermodynamic properties of association obtained recently by microcalorimetry, and the calculated differences in Gibbs free energies of complexation are in excellent agreement with the experimental ones.