Energy harvesting by the flow of a hydrochloric acid-water solution through a carbon nanotube (CNT) is explored using atomistic simulations. Through ion configurations near the CNT wall, the ion drifting velocity is obtained, and the induced voltage along the axial direction is obtained as a function of key material and system parameters, including the applied flow rate, ambient temperature, solution concentration and nanotube diameter. The molecular mechanism of ion hopping and motion is elucidated and related to the variation of material and system parameters.