Hi, I want to calculate the solvation free energy of Wild-type human IAPP (hIAPP) with 37 residues in length that residu26 isoleucine is mutated to proline (ile26pro). I used dual topology in Thermodynamic integration (TI) for calculating salvation free energy. For the solvation free energy calculations I need some parameter as *Sc_alpha*, *Sc_power* and *Sc_power * in* *mdp file.
I also read manual of Dr David van der spoel about salvation free energy and manual of Gromacs. Nevertheless, I couldn’t decide best value for these parameters and my protein. I used the following values in mdp file: free_energy = yes init_lambda = 0.00 sc_alpha = 0.5 sc_power = 1.0 sc_sigma = 0.3 What values do you suggest for these parameters? Thanks very much, Afsaneh Maleki
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