[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:



> 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:


It was designed for an older version of Gromacs, but many of the basic points
still apply.


>         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


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