Empty linear associations accounting for three alpha-CD units and their corresponding pseudorotaxanes have been studied by means of long length molecular dynamics (MD) simulations in a vacuum and in aqueous solution. Results from MD for empty sequences lead to a quite stable arrangement formed by three mutually perpendicular cyclodextrin (CD) units named here as 3P. In such a spatial arrangement, the van der Waals term in the force field is pronounced, accounting for almost 40% of the association energy, which ensures the noticeable stability of the 3P association even in aqueous media. In addition, it can be stated that only the presence of the oligomer forces the CD units to acquire an almost linear association. Mutually perpendicular-based arrangements are the most favorable spatial disposition in aqueous media. We believe this work is the first step toward a more ambitious study including very large CD sequences, aiming to understand the association process in aqueous solution at a molecular level.