At the same time, R 2 drops below 0.5 in all cases, and becomes as small as 0.06 for the β-strand and even smaller than zero for the β-hairpin. While for the quantum-chemical reference values, some dependence of the local-mode frequencies on the position in the peptide chain is still present (e.g., for the polyalanine α-helix, the local modes close to the C-terminus appear at higher wavenumbers), such a dependence is mostly lost in the predictions of the vibrational map. For the remaining two test cases, the 1GPB 3 10 -helix and Trpzip2, the RMSDs are only slightly increased compared to the case of isolated polypeptides. However, the local-mode frequencies now cover a smaller range, which makes the overall correlation appear worse in the plots, and results in an R 2 of 0.22 and of below zero, respectively.