Hi all I have recently generated a PMF curve for pulling a guest molecule into a host. The curve for this process appears fine. Analysis of the histograms are also fine except that some histograms are not centred on their r0 values in the barrier region. To circumvent this I increased the force constant of these windows of which there are three, and constructed the same curve exactly as before, with the only difference being the force constant of the three windows in question. The two profiles are now different (see attached, black has higher force constants for r0n values of 0.16nm,0.24nm,and 0.32nm) but I don't know what one is the most reliable. I expected the barrier to increase with the increased force constant but not the rest of the profile. Has anyone any thoughts on why this might be? Is it O.K to use different force constants for different windows? Is it O.K to have a higher concentration of sampling windows in a specific region than in the rest of the curve? (I haven't done this in this case but I have previously).
Gavin
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