We investigated the scaling of the three models by running calculations on systems of increasing size. To do so, we first converted the protein data bank (PDB) files into Tinker input files using the Tinker tool pdb2xyz. We assigned the parameters using the Amber 99 force field , which is bundled within Tinker. Further information about the input structures is given in table . 997 [104] Table : PDB codes and number of atoms for the structures used in the benchmark (upper part) and in the MD simulations (bottom part).