Traditionally, catalytic processes are calculated using the total energy approach from density functional theory (DFT), and the method to determine the barriers of the adsorption/desorption from DFT calculations is thus still not available. In this work, we choose CO adsorption/desorption on Pt(111) as a model for two reasons. First, it is often a rate-limiting step in many catalytic reactions. Second, the disagreement between the experiment and DFT calculations on the CO adsorption sites of Pt(111) has been known as "the CO puzzle" in the literature, and to further understand the puzzle is desirable. We introduce a molecular dynamics method within the framework of DFT, allowing us to calculate the free energy barriers of adsorption/desorption without experimental inputs. Our results show that the top site is more preferred for CO adsorption in terms of free energy, which agree with experimental work, but in contrast to the traditional DFT total energy calculations. A delocalized nature of CO chemisorption on the hollow site is found, and the key reason for the discrepancy between the free energy simulations and the total energy calculations is identified, which may have some profound implications in total energy calculations in general. © 2018 American Chemical Society.