gmelaugh01 at qub.ac.uk
Mon Sep 6 15:00:37 CEST 2010
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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