Water permeation across various nitrogen-doped double-walled carbon nanotubes (N-DWCNT) has been studied with molecular dynamics simulations to better understand the influence of water-nanopore interaction on the water permeation rate. There exists a threshold interaction energy at around -34.1 kJmol. Over the threshold energy, the water flow through N-DWCNT decreases monotonically with the strengthening of the water-nanotube interaction. The effect on the water flow across the channel is found to be negligible when the interaction energy is weaker than the threshold. The water-nanotube interaction energy can be controlled by doping nitrogen atoms into the nanotube walls. Although the van der Waals interaction energy is much stronger than the electrostatic interaction energy, it is less sensitive to the proportion of doped nitrogen atoms. On the other hand, the electrostatic interaction energy weakens after the initial strengthening when the percentage of doped nitrogen atoms increases to ∼25. The doped nitrogen atoms make less influence on the overall electrostatic interaction energy when the proportion is over 25, due to the repulsions among themselves. Thus, the monotonous strengthening of the van der Waals interaction energy seems to dominate the overall trend of the total interaction energy, whereas the change of the long-range electrostatic interaction energy characterizes the shape of the correlation curve, as the percentage of doped nitrogen atoms increases. © 2012 American Institute of Physics.