The molecular dynamics modeling is widely used for revealing details and calculating quantitative characteristics of biomolecule interactions. The challenge arises when calculating equilibrium characteristics, such as the dissociation constant, that requires expansive computational time until equilibrium is established. In this article, an effective method for such computations is presented alongside with the results of the dissociation constant calculation for the complex of protein CD44 as the receptor and hyaluronan as the ligand. Interaction of the hyaluronan (HA) with its receptor CD44 plays an important role in many cellular and tissue processes, including cell adhesion, regulation of cell growth and migration, inflammation, tumor progression and dissemination. Several therapeutic strategies utilize lipid-based nanoparticles decorated with hyaluronan that targets CD44 expressing tumors. Further progress in the understanding of the mechanism and in the appropriate drug design requires quantitative characterization of the interaction. Here, a specially developed method is used to calculate the dissociation constant K_D for the hyaluronan-CD44 protein interaction and to study its dependence on the length of the HA molecules and on the temperature. Oligomeric forms of the HA (from 2 to 16 monomers in a chain) have been considered. A general tendency for short and medium HA molecules is the decrease of the K_D with the length increase. The results obtained are in good agreement with experimental data on the short-length HA-CD44 interaction. The ligand-receptor affinity, and hence, physiological functions of that interaction, depend on temperature. Importantly, the interaction characteristics at physiological conditions differ significantly from commonly reported data, usually obtained at room temperature. Values of the dissociation constant calculated at T = 20 °C and at T = 36.6 °C differ by a factor from one to three orders of magnitude, depending on the length of HA molecules.