[gmx-users] Umbrella sampling

[XAvier Periole]

My bad, I red to quick and though you had three windows ...
you should follow Justin's advice.

On Mar 31, 2011, at 2:20 PM, Gavin Melaugh wrote:

> 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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