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. I searched the internet to find a study regarding the concentration dependency of the PMF. Is this reasonable? Any suggestions? Regards Ozge Engin
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