When partitioning the protein, ACE-NME caps are added using the original positions for all cap atoms that are already present in the protein, while the remaining hydrogen atom of the methyl groups is added using a fixed C-H bond distance of 1.07 Å. For H-MFCC, the hydrogen cap atoms are added using with a C-H distance of 1.03 Å and an N-H distance of 1.02 Å. Disulfide bridges between amino acids are treated as described earlier .