For the MD simulations, two 24-mer models of amylin 20-29 protofibrils and one 24-mer model of an Aβ 25-35 protofibril were constructed using VMD. For each model, a single βsheet containing 12 peptides was first built and then duplicated and stacked on the initial β-sheet. The putative fibril structures were constructed based on Raman data. For amylin 20-29 , both an antiparallel and parallel β-sheet fibril model were constructed, while only a parallel β-sheet fibril was constructed for Aβ 25-35 . The α-carbons of the two stacked β-sheets were initially separated by 10 Å for each model. Rather than solvate these models with explicit solvent, we opted to use a generalized Born implicit solvent (GBIS) protocol with a dielectric constant of 3.23, mimicking that of the interior of proteins, and an ion concentration consistent with experimental sample preparation. Implicit solvent enabled us to better approximate the environment of an effectively infinite fibril. These models consist of 3336 and 3720 atoms for amylin 20-29 and Aβ 25-35 fibrils, respectively.