[gmx-users] umbrella sampling-Bimodal Histograms

[Aswathy]

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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