Molecular dynamics (MD) simulations are carried out to investigate the permeation of nanometer-sized cylindrical pores connecting two reservoirs, by water molecules and by a reference Lennard-Jones fluid. Water molecules penetrate a channel of fixed length only beyond a minimum radius. Near threshold, permeation is found to be intermittent and sensitive to other physical parameters, including the polarizability of the medium (e.g., a cell membrane) embedding the channel. Once the molecules fill the pore, the confined water exhibits properties (mean density, diffusivity, hydrogen bonding) surprisingly close to those of the bulk. The intermittent behavior near the threshold is analyzed in terms of a Landau-like grand potential regarded as a function of the pore occupancy. The grand potential, which is determined using a biased sampling technique, generally exhibits two minima, associated with the "empty" and "filled" states, separated by a potential barrier (transition state). No intermittent filling of identical pores is observed in the possible case of the reference Lennard-Jones fluid over a wide range of physical conditions, pointing to the specific role of hydrogen bonding for intermittent behavior. A careful analysis of the MD-generated configurations shows that the filled state nucleates around a chain of hydrogen-bonded molecules spanning the pore. (C) 2003 American Institute of Physics.