Single-molecular systems are a test bed to analyze to what extent thermodynamics applies when the size of the system is drastically reduced. Isometric and isotensional single-molecule stretching experiments and their theoretical interpretations have shown the lack of a thermodynamic limit at those scales and the nonequivalence between their corresponding statistical ensembles. This disparity between thermodynamic results obtained in both experimental protocols can also be observed in entropy production, as previous theoretical results have shown. In this work, we present results from molecular dynamics simulations of stretching of a typical polymer, polyethylene-oxide, where this framework is applied to obtain friction coefficients associated with stretching at the two different statistical ensembles for two different system sizes, from which the entropy production follows. In the smallest system, they are different up to a factor of 2, and for the bigger system, the difference is smaller, as predicted. In this way, we provide numerical evidence that a thermodynamic description is still meaningful for the case of single-molecule stretching.