[gmx-users] Sampling windows

[Gavin Melaugh]

Hi Xavier

Many thanks. Two more quick questions (both refering to barrier region):
Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap? Obviously there is a
compromise between the size of the constant and the number of windows.
If I increase the force constant and number of windows to obtain a high
density of sampling, does this give a more accurate curve?

Gavin

XAvier Periole wrote:
>
> 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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>