Cryptophanes are aromatic hosts which bind a variety of guests. Here, we describe a 25 ns molecular dynamics simulation of a particular cryptophane host-guest complex in water. The cryptophane used in this study was used previously in a 20 ns molecular dynamics simulation to describe the fluctuations of the uncomplexed host. This cryptophane features three pores which open onto a cavity where the guests bind. In the current study, tetramethylammonium ion (TMA(+)) has been placed within the cryptophane cavity to form the host-guest complex. The molecular dynamics simulation in combination with a surfacing algorithm provides information on the frequency with which the cryptophane pores open wide enough to admit or release guest molecules of any given size. We discuss these fluctuations and their possible consequences for binding kinetics, making comparisons between the cryptophane and the cryptophane-TMA(+) complex.