The paper is organized as follows. In Section II we begin first by reviewing the exact factorization approach and the trajectory-based methods derived from it, then examine energy conservation in these methods and introduce the modified CTMQC-E algorithm. Section III is devoted to numerical simulations of the molecular models comparing the performance of CTMQC-E with respect to CTMQC as well as surface-hopping with energy-based decoherence correction. Section IV at last provides the main conclusions of our work as well as an outlook.