[gmx-users] Free Energy tutorial - choosing number of solvent molecules

[Justin A. Lemkul]

Fabian Casteblanco wrote:
> Hello all,
> 
> I'm running the same process from the free energy tutorial by Justin 
> Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html.
> 
> How did the number of solvent particles get chosen (in the tutorial, 210 
> molecules were chosen)?   I seem to be getting slightly different 

If memory serves, I reproduced what was in the original paper, but do check.

> results (ranging from as small as 200 J/mol to about 5 kJ/mol depending 
> on how many molecules I choose (ranging for example from 210 ethanol 
> molecules to about 610 ethanol molecules for the largest energy 
> difference change of about 5 kJ).   I keep running tests to see if there 
> is some sort of minimum atom number to get steady consistent numbers but 
> I can't seem to find it.  When I plot for example the bar.xvg & 
> barint.xvg for both sets to see where the lines don't match up, its 
> usually one or two points that differ slightly which cause the free 
> energies in the end to be slightly different.    I seem to be noticing 
> too that the more atoms I use, the free energy gets a little bit lower.
> 
> Does anybody have any experience with this?
> 

How long are your simulations?  I have experienced the case (using a 
water-octanol solvent mixture) where the initial configuration made a big 
difference in the result, so longer simulations and multiple configurations for 
the solvent were necessary to get reliable averages.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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