In order to enable the efficient use of replica exchange molecular dynamics(REMD) in multiscale and explicit solvent simulations, we introduce a Replica-Exchange-with-Tunneling (RET) method by integrating ideas of hybrid MC/MD into the replica-exchange protocol. For a 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.