The cause of Alzheimer's disease is related to aggregates such as oligomers and amyloid fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies have been conducted to understand the molecular mechanism of the formation and disruption of Aβ aggregates. In this Perspective, the MD simulation studies are classified into four categories, focusing on the target systems: aggregation of Aβ peptides in bulk solution, Aβ aggregation at the interface, aggregation inhibitor against Aβ peptides, and nonequilibrium MD simulation of Aβ aggregates. MD simulation studies in these categories are first reviewed. Future perspectives in each category are then presented. Finally, the overall perspective is presented on how MD simulations of Aβ aggregates can be utilized for developing Alzheimer's disease treatment.