[gmx-users] Solvation free energy

afsaneh maleki 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,
Afsaneh Maleki
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