Cello-oligosaccharide intermediates are formed during the enzymatic hydrolysis of cellulose. Re-adsorption of these cello-oligomers on the cellulose crystal surface hinders the enzymatic hydrolysis step in the conversion of lignocellulosic biomass to biofuel. The knowledge of energetics as well as the mechanism of desorption of cello-oligosaccharides from cellulose crystal surface is thus important for optimizing the enzymatic hydrolysis process conditions. In this study, we have used molecular dynamics simulations to calculate the free energy of desorption of a short cello-oligosaccharide from the cellulose Iß crystal surface. Specifically, we have calculated the free energy of desorption of cellohexaose from the (100) and the (110) surfaces of this cellulose crystal. In complex systems such as the one under consideration, there are several choices for defining the reaction coordinate that is required for performing these free energy simulations. We have compared the results obtained by the usage of two differentreaction coordinates in our calculations. Our results show that, in general, the free energy of desorption of cellohexaose from the cellulose crystal surface exhibits a step-wise increase, corresponding to sequential peeling of the adsorbed glucose residues from the cellulose crystal surface.