[gmx-users] Sampling windows

[Gavin Melaugh]

Hi Xavier

Thanks very much for your time. That has mad things very clear

Gavin

Avier Periole wrote:
>
> On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote:
>
>> 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?
> No! The force constant used does not affect the PMF or the barrier.
> Neither
> does the number of windows used. The only thing that can affect your
> PMF is a change in the sampling you put in ...
>> Obviously there is a
>> compromise between the size of the constant and the number of windows.
> True! And the objective being to get equilibrated distribution with
> reasonable
> overlaps.
>> If I increase the force constant and number of windows to obtain a high
>> density of sampling, does this give a more accurate curve?
> No! The only thing you need is to sample everything. Actually putting a
> strong force constant might have the side effect to trap your system and
> then you do not sample the "free" degrees of freedom! With weak force
> constant you may have to wait very long to obtain an equilibrated
> distribution.
>
> XAvier.
>>
>> 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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>>
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>