[gmx-users] Umbrella sampling

[Gavin Melaugh]

Here is also the sample .mdp file

chris.neale at utoronto.ca wrote:
> can you show us your mdp and the pmf and the histograms for the data
> that you put into wham? It's a lot easier to diagnose with the real data.
>
> In the general case where umbrellas are spaced equally along your
> reaction coordinate, sampling overlap between umbrellas will always
> decrease anywhere the PMF is concave down, such as your barrier
> region. I would suggest adding windows at every 0.005 nm spanning the
> region that you consider to have a sampling problem (e.g. 0.76 to 0.83
> ?) and use a much stronger force constant here (e.g. 2-3 times as
> strong as you used for umbrellas with 0.02 nm spacing). You have
> identified a problem, so my suggestion is to not bother fiddling with
> adding one extra replica but sample that region to death with strong
> force constants. I presume that this will not impact your overall
> efficiency too much if the reaction coordinate is long overall.
>
> Finally, you will need to evaluate the convergence of your PMF overall
> and perhaps of this region in particular, especially if you want to
> know the dG to cross it or between two low energy states on either
> side of it.
>
> Chris.
>
> -- original message --
>
>
> 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).
>
> 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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>

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