This contribution concerns the application of the thermodynamic-integration approach to crystalline structures. We calculate the defect Helmholtz energy of a single comonomer inclusion into the crystal structure of the host polymer via molecular-dynamics simulations. It was found that prior to the commonly applied scaling of the force field parameters, an additional scaling of some bond lengths and a modification of the short-distance nonbonded interaction potentials were necessary to avoid singularities and numerical instabilities during the free-energy calculations. The resulting defect Helmholtz energies for single inclusions in the system poly(ethylene terephthalate-co-2,6-dicarboxy naphthanoate) were considerably larger than the thermal energy and prohibit comonomer inclusion.