Molecular dynamics (MD) simulations were performed for "channel type" polyrotaxanes with alpha-cyclodextrins (alpha-CDs) threaded onto monodisperse chains of poly(thylene glycol) (PEG). The polymer captures as much alpha-CD as its length permits, forming a close-packed structure from the one end to the other. The van der Waals interactions are the main source of the stabilization of these polyrotaxanes. Hydrogen bonds between successive alpha-CDs slightly favor head-to-head, tail-to-tail sequences over head-to-tail sequences. The alpha-CDs in polyrotaxanes are more symmetric and less distorted than the isolated alpha-CDs. The PEG in the polyrotaxane is more extended than an unperturbed chain, because it has a larger population of trans states at internal bonds.