[gmx-users] Umbrella sampling

[XAvier Periole]

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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