The complex structural pattern described by water molecules in the channels of the large-pore VPI-5 aluminophosphate has been investigated through Car-Parrinello ab initio molecular dynamics simulations. Water molecules occupy crystallographic positions but considerably rotate and oscillate around their equilibrium positions. The extended network of strong hydrogen bonds among water in the channels leads to nonnegligible collective motions. The conformation of the triple helix formed by water molecules has been thoroughly examined; the helices run close to the channel walls and avoid the channel center. The high thermal motion of the water molecules makes such chains rather flexible and the helices are not easily detectable during the dynamics, but their shape emerges only when the average atomic positions are considered.