[gmx-users] Umbrella sampling - regd

[ramesh cheerla]

Dear Justin,

                Thank you very much for your quick reply.

Regards,
Ramesh.



On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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