[gmx-users] Solvation free energy
maleki.afsaneh at gmail.com
Wed May 19 13:22:52 CEST 2010
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,
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