Conductive polymers have several applications such as in flexible displays, solar cells, and biomedical sensors. An inclusion complex of a conductive polymer and cyclodextrin is desired for some applications such as for molecular wires. In this study, different orientations of beta-cyclodextrin rings on a single polyaniline (PANI) chain in an alternating emeraldine form were simulated using molecular dynamics. The simulations were performed in an implicit solvent environment that corresponds to experimental conditions. When the larger opening of the beta-cyclodextrin toroids face the same direction, the cyclodextrins tend to repel each other. Alternating the orientation of the beta-cyclodextrins on the chain causes the beta-cyclodextrin rings to be more attractive to one another and form pairs or stacks of rings. These simulations explain how the beta-cyclodextrins can be used to shield the polyaniline from outside chemical action by analyzing the PANI/cyclodextrin interactions from a molecular perspective.