Figure 2.

Simulation strategy for linking MD structures with experimental IR spectra. Individual peptide groups and their associated amide I transition dipoles are identified in structures sampled from MD simulations. A local mode Hamiltonian is parametrized from the structure using the molecular electric field to set the diagonal site frequencies and off-diagonal couplings between sites. The delocalized eigenstates and their corresponding transition dipole moments are used to calculate the IR spectrum and use doorway modes to visualize the vibrations.