[gmx-users] Umbrella sampling - regd

[Justin Lemkul]

On 1/1/13 11:48 PM, ramesh cheerla wrote:
> Dear Gromacs users,
>
>                                       I am performing  umbrella sampling
> simulations by selecting configurations with spacing window of  0.02nm from
> pulling simulations with the following options in .mdp file to get PMF
> along a axis for permeation of ion through a channel.
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = position  ; simple distance increase
> pull_dim       = N Y N
> pull_vec1        = 0 -1 0
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = FIXEDATOM
> pull_group1     = SMDATOM
> pull_rate1      = 0.0     ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 2000      ; kJ mol^-1 nm^-2
> pull_init1      = 0
>
> And   am using g_wham to get PMF, while using g_wham,  am getting the
> warnings like :
> WARNING, no data point in bin 139 (z=-0.492557) !
> You may not get a reasonable profile. Check your histograms!
> Warning, poor sampling bin 193 (z=-0.364322). Check your histograms!
> Warning, poor sampling bin 194 (z=-0.361947). Check your histograms!
> Warning, poor sampling bin 195 (z=-0.359572). Check your histograms!
> Warning, poor sampling bin 196 (z=-0.357197). Check your histograms!
> Warning, poor sampling bin 197 (z=-0.354823). Check your histograms!
> Warning, poor sampling bin 198 (z=-0.352448). Check your histograms!
> Warning, poor sampling bin 199 (z=-0.350073). Check your histograms!
> Initialized rapid wham stuff (contrib tolerance 6.66667e-08)
> Evaluating only 2115 of 3000 expressions.
> I have checked my histograms and PMF profile, by doing so I have understood
> that histograms overlapping is restricted to only some regions and there is
> no histograms at all in some regions i.e severe sampling problems at
> barrier regions.  here I am sending the link that containing PMF profile
> that I have obtained,  http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg
>
> Can anybody tell me how can I get proper sampling at barrier regions is
> there any efficient way to do this, how about meta dynamics with suitable
> CV (collective variable) ? .
>
>

Use a stronger force constant in these barrier regions to restrict the movement 
along the reaction coordinate.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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