[gmx-users] Sampling windows

[XAvier Periole]

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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>
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