Hi All I have generated a potential of mean force curve for two cage molecules. The profile of the curve is very good apart from the fact that the repulsive part of the curve doesn't go above zero. My attractive tail therefore appears higher than the repulsive part. The histograms are very well behaved. I use a force constant of 1000 for all sampling windows. At closer distances between the centres of mass (the repulsive part), the mean value is not centred around the ref distance, I assume due to repulsion. To circumvent this I have increased the force constant to 10000 for the last sample distance. My PMF curve has now a constant value of zero even though the histograms are fine. Why is this so ?
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