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

Fabian Casteblanco fabian.casteblanco at gmail.com
Thu Jan 26 17:21:21 CET 2012

Hello all,

I'm running the same process from the free energy tutorial by Justin

How did the number of solvent particles get chosen (in the tutorial, 210
molecules were chosen)?   I seem to be getting slightly different 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?


*Best regards,*
*Fabian F. Casteblanco*
*Rutgers University -- *
*C: +908 917 0723*
*E:  **fabian.casteblanco at gmail.com* <fabian.casteblanco at gmail.com>
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