We carried out molecular dynamics (MD) simulations with the AMBER force field for four pairs of spherical dimers of different size (neopentane, bicyclooctane, adamantane, and fullerene‐C60) using the TIP3P model of water as solvent. For comparison, we performed MD simulations for a linear molecule of n‐pentane at the same conditions. To assess the entropy contribution to the Gibbs free energy, MD simulations were run at three different temperatures of 273 K, 323 K, and 348 K, respectively, using umbrella‐sampling/the WHAM method. The stability of dimers is described by a potential of mean force (PMF). The shape of PMF curves for hydrophobic interactions is characteristic, and entails a contact minimum, a solvent‐separated minimum, and a desolvation maximum. The depth and position of the contact minimum for each pair change with the size of the nonpolar particle, and are consequently shifted to a larger distance for larger molecules. Additionally, the Lennard–Jones contribution to the PMF increases simultaneously with an increase in particle size. For a linear dimer, the contact minimum is shifted to a shorter distance than it is for spherical systems with the same number of carbon atoms. The contact minima on PMF curves increase with temperature, suggesting that the association entropy is positive. Dimensionless PMF curves showed a low dependency (near contact minima regions) on temperature, as the association entropy is low. Copyright © 2014 John Wiley & Sons, Ltd.