Hydrogen atoms were added using OpenBabel , considering a neutral protonation state for each amino acids. In the process of partitioning the proteins, ACE-NME caps are added using the original positions for all cap atoms that are already present in the protein, while the remaining hydrogen atoms of the methyl groups are added using a fixed C-H bond distance of 1.07 Å. Disulfide bridges between amino acids are capped with methylsulfide groups. The resulting dimethyldisulfide cap molecules are treated analogously to the other cap molecules in the many-body corrections.