[gmx-users] number of water molecules affects the PMF
x.periole at rug.nl
Tue Jun 1 21:41:42 CEST 2010
On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote:
> Hi all,
> I am trying to calculate the potential of mean force between the two
> hydrophobic dipeptides (phenylalanine) in bulk water via constraint
> pulling simulations. First, I calculated the mean force at each of
> the constraint points, and then I integrated the mean force curve to
> get the PMF.
> In order to test how big the effect of the number of water molecules
> on the calculated PMF I performed two sets of simulations which
> differed from each other in terms of only the number of water
> molecules. I used 9000 water molecules in one set, and 7000 in the
> other. The overall PMF for the latter was steeper than the former,
> as I expected before. However, the minimum point for the former was
> around 2.79 kJ/mol, and for the latter 5.30 kJ/mol. I did not think
> that the difference should not be that much since there is not a big
> difference between the number of water molecules between the two sets.
Could it be that the difference is within the error ? What happens if
cut your data of each simulation in two pieces? In other words are you
> I searched the internet to find a study regarding the concentration
> dependency of the PMF.
> Is this reasonable? Any suggestions?
> Ozge Engin
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