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

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 27 02:40:44 CET 2012

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 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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