“…This possibility to treat each residue type by a different value of R i is a simple way to partially account for the nonspecific contributions from the hydrophobic effect in the model. ,, Such different radii help to both preserve the macromolecular hydrophobic moments and to guide the orientation at short separation distances. Other details, justifications, validation, pros, and cons are given elsewhere. ,,,,, In short, the full configurational energy of the system [ U ({ r k })] combining a screened Coulombic term (first term) with an LJ one (second term) is given by where { r k } are amino acid coordinates at a given configuration, z i and z j are the valences of the amino acids i and j as defined by the titration scheme, e is the elementary charge ( e = 1.602 × 10 –19 C), κ is the modified inverse Debye length, , r ij is the separation distance between beads i and j , ε 0 is the dielectric constant of the vacuum (ε 0 = 8.854 × 10 –12 C 2 /Nm 2 ), ε is the dielectric constant of the medium assumed to be equal to 78.7 to mimic an aqueous solution at temperature T equals to 298 K, ε LJ is a parameter that regulates the attractive forces in the system, ,, σ ij is given by the Lorentz–Berthelot rule from the radius of beads i and j ( R i and R j ), and N is the total number of beads. The universal value of 0.124 kJ/mol was chosen for ε LJ . ,, This should be equivalent to a Hamaker constant of ca.…”