A 0.76 ns molecular dynamics simulation has been performed on a self-assembled peptide nanotube in water. The peptide structure is composed of 10 beta-sheet-Like hydrogen-bonded stacks of the flat ring-shaped cyclic D,L octapeptide subunit cyclo[-(Gln-D-Ala-Glu-D-Ala-)(4)]. The synthesis and self-assembly of such nanotubes and their ability to form remarkably transport-efficient transmembrane ion channels and pore structures have been reported previously. During the simulation, the tubular construct retains its structural integrity with only slight distortion at the outer ends. Water molecules in the tube tend to be organized in alternating zones of one water near the plane of the backbone C-alpha atoms and two waters near the plane midway between two adjacent peptide subunits-the idealized 1-2 water structure. On average, 32.8 water molecules are found in the tube during the data-gathering phase of the simulation. Analysis of the motion of water molecules in the tube gives a diffusion constant of 0.44 x 10(-5) cm(2) s(-1), which is approximately one-sixth of the self-diffusion constant of bulk water and much faster than either molecular dynamics or experimental measurements of the diffusion constant of water in the structurally related gramicidin A transmembrane channel. A detailed examination of the tube-water trajectories shows that water molecules can pass by one another in contrast to the single-file diffusion occurring in gramicidin A. We suggest that water diffusion can be understood as a series of "hops" between zones which can cause transient local deviations from the ideal number of water molecules in a zone. A slight excess of the average water population over the "ideal" number of water molecules expected from the alternating 1-2 structure suggests that diffusion in the tubes may be enhanced in a manner roughly analogous to the enhanced conductivity of n-type semiconductors due to doping.