The starting molecular structures for the four polyalanine test cases were constructed using VMD with the Molefacture plugin by using pre-defined backbone angles. For the 3 10 -helix cutout from glycogen phosphorylase B, we used residues 515 to 524 from the PDB structure (PDB-Code: 1GPB), and for the tryptophan zipper 2, we also used the PDB structure as starting point (PDB-Code: 1LE1) All structures were capped with acetyl group (ACE) at the N-termini and an N-methyl group at the C-termini.