[gmx-users] profile

[Gavin Melaugh]

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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