Recently, effective one-dimensional configuration coordinate diagrams have been utilized to calculate the line shapes of luminescence spectra and nonradiative carrier capture coefficients via point defects. Their calculations necessitate accurate total energies as a function of configuration coordinates. Although supercells under periodic boundary conditions are commonly employed, the spurious cell size effects have not been previously considered. In this study, we have proposed a correction energy formalism and verified its effectiveness by applying it to a nitrogen vacancy in GaN.