State-of-the-art directed self-assembly (DSA) of block copolymer (BCP) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication. The defect free energy of a dislocation pair or jog defect, one of the most common defects found in BCP-DSA, is calculated via thermodynamic integration using a coarse-grained molecular dynamics model as a function of and the degree of polymerization (). It is found that is not the best predictor of defect free energy and that a single value can yield vastly different free energies when and are different. Defect free energy was highly dependent on defect location relative to the underlayer, and free energy differences were found among the three possible defect locations on a 1:3 guiding pattern. It was found that increasing molar mass dispersity () significantly reduced defect free energy. Extrapolating from up to 1.5 suggests that the defect will occur in equal proportions to the defect free state at a of around 1.6 for this system. It was found that long chains tended to concentrate near the defect and stabilize the defect.