Molecular dynamics simulations have been performed at 223, 300, and 373 K for polyethylene in the inclusion complex with perhydrotriphenylene. The system contains 90 molecules of perhydrotriphenylene, arranged in 6 stacks of 15 molecules each, and one molecule of n-tetracontane, C40H82. These 91 molecules have 4442 atoms. The internal CH2-CH2 bonds in the n-tetracontane have a strong preference for the trans state. However, the nearly complete suppression of trans --> gauche transitions does not imply that the chain is quiescent in the channel. Instead it exhibits a high degree of internal flexibility via processes that have a low activation energy. The activation energy for rotation of a C-H bond vector about the long axis is less than 1 kcal mol-1. The mobility of the C-H bond vectors is greater at the ends than in the middle of the chain. The angular distributions of the internal C-H bond vectors about the long axis of the channel are nearly randomized within 1 ns at 300 K.