Abstract Explicit solvent molecular dynamics (MD) simulations on the triple helix of the polysaccharide Scleroglucan (Sclg) at two temperatures (273 and 300 K) were carried out. Owing to the complexity of the system, a united-atom force field, based on the properly modified GROMACS parameters, was adopted. To test these parameters for our system, MD simulations of the two disaccharidic units, representing the main chain and the side-chain linkages of the Sclg repeating unit, were performed and the results were compared with the literature data. The simulated triple helix of Sclg retained the main experimentally determined features of the polymer. The residence times of the solvent molecules at 273 and 300 K were analyzed. The results show that the more internal water molecules, interacting with the core of the Sclg triplex are not influenced substantially by changing the temperature, on the contrary the water molecules, interacting with the side-chain glucose residues show more significant differences. These data suggest that the more external water molecules, interacting with the side chain, play a major role in the conformational transition experimentally observed at low temperature.