Aggregates of the amyloid-β (Aβ) peptide are implicated as a causative substance in Alzheimer's disease. Molecular dynamics simulations provide valuable contributions for elucidating the conformational transitions of monomeric and aggregated forms of Aβ be it in solution or in the presence of other molecules. Here, we study the effects of four different glycosaminoglycans (GAGs), three sulfated ones and a nonsulfated one, on the aggregation of Aβ16-22. From experiments, it has been suggested that GAGs, which belong to the main components of the brain's extracellular space, favor amyloid fibril formation. Our simulation results reveal that the binding of Aβ16-22 to the GAGs is driven by electrostatic attraction between the negative GAG charges and the positively charged K16 of Aβ16-22. While these interactions have only minor effects on the GAG and Aβ16-22 conformations at the 1 Aβ16-22/1 GAG ratio, at the 2:2 stoichiometry the aggregation of Aβ16-22 is considerably changed. In solution, the aggregation of Aβ16-22 is strongly influenced by K16-E22 attraction, leading to antiparallel β-sheets. In the presence of GAGs, on the other hand, the interaction of K16 with the GAGs increases the importance of the hydrophobic interactions during Aβ16-22 aggregation, which in turn yields parallel alignments. A templating and ordering effect of the GAGs on the Aβ16-22 aggregates is observed. In summary, this study provides new insight at the atomic level on GAG-amyloid interactions, strengthening the view that sulfation of the GAGs plays a major role in this context.