On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:
Hi Xavier
Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased
force
constant (note I have only increased the force constant of the windows
in the barrier region).
Force constant =1000, Force constant in barrier region = 5000
The barrier increases due to better sampling in this region
(expected),
but the rest of the curve in 2) is shifted upward compared to curve
1).
Why is this so when the only difference is the increased number of
windows and force constant in one region?
the relative position of the regions on the left and right of your
"barrier"
region is completely depending on the barrier region!
you may have overestimated the difference between bound/unbound states
because the energy barrier region was not sampled.
Note also that cure one is simply wrong so comparing to it is dangerous.
You have to be careful that you might still not have a converged
sampling:
you might have overlap of your histograms on the reaction coordinate but
other degrees of freedom are not fully sampled ... that might result
in a
funny and wrong profile. You might want to look at your simulations for
funny things ...
Gavin
XAvier Periole wrote:
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
Dear all
I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems
fine,
but there are no overlaps between histograms in the barrier
region. To
circumvent this I have added more windows in this region and to
ensure
sampling have increased the force constant only in this region. The
windows in this problematic region are now not equally spaced.
Does this
matter for g_WHAM?
Nope it does not matter.
Could someone please reply to me on this matter as it
has been a sticking point for me for quite sometime?
Many thanks
Gavin
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