Jinyao Wang wrote:
hi,gmx-users
I am repeating the calculation of the toluene in water using GMX 4.0.4. I
have read the maillist about the the solvation free energy of toluene in
water. I know that the sc-power and the point lambda are very important. So I
set sc-power=2 and 25 lambda points.
Then you should read more thoroughly. Have a look at Berk's opinion on setting
sc-power = 2:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040615.html
<snip>
free_energy = yes
init_lambda = 0.88
> sc-alpha = 1.51
> sc-power = 2.0
And what motivated your choice of sc-alpha? It makes no sense to me. Typically
a value of 0.6 is used. You may want to consult the tutorial designed to
calculate the deltaG of solvation for toluene:
http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html
It was designed for an older version of Gromacs, but many of the basic points
still apply.
-Justin
Jinyao Wang [email protected] 2009-09-15
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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