[gmx-users] umbrella sampling-Bimodal Histograms

[Aswathy]

I took initial 300 as equilibration,Now it seems fine.
Thank you ..

On Tue, Jun 22, 2010 at 9:21 AM, <chris.neale at utoronto.ca> wrote:

> Take that replica on the left that shows a bimodal histogram. Now plot a
> time series of the displacement: x-axis = time and y-axis = displacement
> along reaction coord. Is it jumping back and forth between two regions of
> sampling? Probably not... more likely it starts near one maximum and
> transitions to another maximum.
>
> If this is true then it simply means that you have not equilibrated enough.
> Run longer and cut some of the initial sampling.
>
> Chris.
>
> -- original message --
>
> I am doing US . Yes, histograms of population densities along the reaction
> coordinate. Please find the pull settings. Sampled for 800ps.(nsteps =
> 400000). Pull_init will vary for each frame, depends on the window spacing.
>
> pull                     = umbrella
> pull_geometry            = position
> pull_dim                 =  N N Y
> pull_start               = no
> pull_nstxout             =  10
> pull_nstfout             =  10
> pull_ngroups             =  1
> pull_group0              =  U_ref
> pull_pbcatom0            = 0
> pull_group1              =  r_C1
> pull_pbcatom1            = 0
> pull_init1               =  0 0 0.1
> pull_k1                  =  1000
> pull_rate1               = 0
> pull_vec1                =  0 0 0
>
> Please check this link for my histograms
>
>
> https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en
>
> I would greatly appreciate our suggestions.
>
> Thank you,
> -Aswathy
>
> On Mon, Jun 21, 2010 at 8:14 PM, <chris.neale at utoronto.ca> wrote:
>
>  Please clarify:
>>
>> Are doing SMD or are you doing US? If you're doing SMD then you should not
>> be using WHAM and you should not really be able to generate any sampling
>> histograms.
>>
>> Are the histograms that you are referring to population densities of the
>> sampling along your reaction coordinate?
>>
>> My guess -- if you're doing US -- is that you have some incorrect pull
>> group settings. Bimodal distributions are indeed possible, but should
>> require very long sampling times to achieve, and I doubt that you are at
>> those times yet. Your Fc is fine. Post your pull settings.
>>
>> Chris.
>>
>> -- original message --
>>
>> When i did the Umbrella sampling of frames from an SMD (of ligand
>> transport), I am getting bimodal histograms in some cases.
>>
>> Do you think this is because , the force constant that i used is very low
>> (i
>> used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my
>> PMF result? Do I need to repeat the sampling again with another pull_k1
>> value(higher value)?
>>
>
>
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-- 
Aswathy
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