[gmx-users] number of water molecules affects the PMF

Ozge Engin ozge.engin at gmail.com
Tue Jun 1 21:13:21 CEST 2010

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

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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