The results of molecular dynamics (MD) simulations are compared to transition state theory estimations for formation of conformational defects in a polymer crystal. The rates of conformational defect formation and destruction are obtained in terms of a distribution over possible conformational states. The rate constant obtained by this method, when normalized by the number of possible defect sites, is independent of the size of the system, in apparent contrast with the results of MD simulations. The difference is interpreted in tetras of the effective temperature of the MD calculation.