A method of operating an HVAC system using a controller includes predicting a first predicted temperature of an enclosed space during an unoccupied time with the HVAC system off. The controller determines if the first predicted temperature is less than a set-point temperature. Responsive to a determination that the first predicted temperature is less than the set-point temperature, the controller predicts a second predicted temperature of the enclosed space if the HVAC system is operated for a first runtime. The controller determines if the second predicted temperature is less than the set-point temperature and, responsive to a determination that the second predicted temperature is not less than the set-point temperature, the controller operates the HVAC system for the first runtime.