We introduce Replica-Exchange-with-Tunneling (RET) simulations as a tool for studies of the conversion between polymorphic amyloids. For the 11-residue amyloid-forming cylindrin peptide we show that this technique allows for a more efficient sampling of the formation and interconversion between fibril-like and barrel-like assemblies. We describe a protocol for optimized analysis of RET simulations that allows us to propose a mechanism for formation and interconversion between various cylindrin assemblies. Especially, we show that an interchain salt bridge between residues K3 and D7 is crucial for formation of the barrel structure.