[gmx-users] Sampling windows

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jan 5 17:01:39 CET 2011

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?


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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