[gmx-users] Umbrella sampling

[Gavin Melaugh]

Thanks Justin for the reply

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Sorry I am not sure that I follow. Will the window with r0 =0.80 giving
>> the distribution centred around 0.78nm not drive my free energy profile
>> up. If I remove this window prior to running g_wham the free energy goes
>> down. Should I increase the force constant so that the mean of the
>> window is 0.80nm (bearing in mind that this is near the barrier region).
>>
>
> If you have an incomplete or otherwise discontinuous free energy
> profile, then you won't get a correct result, but it's not simply due
> to "oversampling" one region.  It's that the "oversampling" results in
> "undersampling" another region.  Increasing the force constant for the
> window centered around 0.80 nm should work.
>
> -Justin
>
>> Gavin
>> XAvier Periole wrote:
>>> You can present the data differently:
>>> you have two windows at 0.78 nm giving different distribution.
>>>
>>> That indicates these windows are not converged. Does not mean
>>> that the others (0.80 nm) are converged :))
>>>
>>> On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote:
>>>
>>>> Hi Xavier
>>>>
>>>> Thanks for the reply. With respect to your answer of my first query.
>>>> What if you had two windows practically on top of each other, but one
>>>> was not supposed to be there. e.g A window with r0 of 0.80 nm and
>>>> centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm.
>>>>
>>>> Gavin
>>>>
>>>> XAvier Periole wrote:
>>>>> On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote:
>>>>>
>>>>>> Hi All
>>>>>>
>>>>>> I have generated several PMF curves for the one system using
>>>>>> umbrella
>>>>>> sampling. In the first part of the curve (barrier region) I use a
>>>>>> high
>>>>>> force constant with small intervals between the windows. The latter
>>>>>> part
>>>>>> of the curve I use a lower force constant with larger window
>>>>>> spacing.
>>>>>> Anyway I have a few issues that I need clarifying:
>>>>>> 1 - Can you have too much overlap between windows?
>>>>> no, there no such a thing of too much overlap :)) You could even put
>>>>> two identical windows with same 100% overlap ... no problem.
>>>>>> 2 - Does the distribution at each window have to centered around the
>>>>>> desired r0? (If not does this affect the free energy?)
>>>>> The deviation of the distribution from the r0 is what dictates the
>>>>> profile. The more away from the disired r0 the higher the free energy
>>>>> of the system.
>>>>>> 3- If you over sample one particular window, will it affect the
>>>>>> curve?
>>>>> There is no such a thing of over sampling ... the only thing you can
>>>>> have is not enough sampling.
>>>>>> Many thanks
>>>>>>
>>>>>> GAvin
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>