We investigate the slip properties of water confined in graphite-like nanochannels by non-equilibrium molecular dynamics simulations, with the aim of identifying and analyze separately the influence of different physical quantities on the slip length. In a system under confinement but connected to a reservoir of fluid, the chemical potential is the natural control parameter: we show that two nanochannels characterized by the same macroscopic contact angle --but a different microscopic surface potential-- do not exhibit the same slip length unless the chemical potential of water in the two channels is matched. Some methodological issues related to the preparation of samples for the comparative analysis in confined geometries are also discussed.