[gmx-users] the problem about the calculation free energy of the toluene in water
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 15 12:30:00 CEST 2009
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 wangjy at ciac.jl.cn 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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