The influence of the size, composition, and atomic distribution of linear guests on β-cyclodextrin inclusion complex formation is clarified by means of a molecular dynamics simulation at constant temperature. The intermolecular energy is modelled by a Lennard-Jones potential, where the molecular composition is represented by various parameters and by a continuum description of the guest and cavity walls. It is concluded that the parameters related to the atomic size require minimum values for the confinement of linear molecules inside the cavity. The isomer with optimal affinity for β-cyclodextrin as predicted by the free energy presents an asymmetrical molecular structure, and the position probability density shows that the isomer tends to insert the portion with largest atoms into the cavity, although the preferential binding site of the guest is not always located in regions of the host with maximum discriminatory power.