Dear Charmm Users,
As we known, in traditional generalized Born (GB) model, the hydrophobic effect is considered by taking the solvent accessible surface area (SASA) as a proxy of the its extend in energy. The nonpolar solvation free energy isn't the function of coordinate, so the hydrophobic force isnot obtained by the derivative of energy with respect to its coordinate. The model may be controversial because we only account for its impact in energy and the hydrophobic force is neglected in MD simulation using AMBER software. In the charmm, is the nonpolar solvation free energy also calculated by the aSASA+b? Is the hydrophobic force considered in MD, if yes, how to add the hydrophobic force in every MD step? Thank you very much !