[gmx-users] the problem about the calculation free energy of the toluene in water

[Justin A. Lemkul]

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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