During the minimization and equilibration simulations, structural constraints obtained from the Raman experimental data were applied to the 24-mer fibril models using NAMD's Collective Variable functionality. In particular, the ψ-angles of the peptides were harmonically restrained about the ψangle peaks we observe experimentally (150°amylin 20-29 polymorph 1 and 139°for amylin 20-29 polymorph 2 and Aβ 25-35 ). The angle between peptide carbonyl bonds and the fibril long axis was harmonically constrained to the values obtained experimentally. Additionally, the constraint force constants were tuned to reproduce the experimentally obtained ψangle and C--O bond angle distributions. The fibril axes were approximated in these models by using VMD to calculate the inertial tensor of the α-carbons and extracting the principal components. The fibril long axes were taken as the resulting principal component perpendicular to the peptides. They were calculated separately for every frame of the simulation trajectories, as atomic fluctuations in the fibrils cause small changes to the axis vectors.