[gmx-users] Umbrella sampling - regd

[ramesh cheerla]

Dear Justin,

I am very thankful to you for your reply, you are correct, I have plotted
the histo.xvg file in wrong manner. After plotting histograms in correct
manner I have realized that my sampling is very poor as histograms and
there overlapping is restricted to some regions only,  no histograms in
some areas along reaction co-ordinate.
I am not sure whether this lack of  sampling is due to  inappropriate
selection of pulled configurations or  inappropriate pull geometry.
However I will try as per your suggestion and get back to you.

Thank you,

Regards,
Ramesh.



On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/26/12 1:03 AM, ramesh cheerla wrote:
>
>> Dear Gromacs users,
>>
>>
>>       I am calculating  PMF for the ion permeation through a tunnel, using
>> umbrella sampling. In my system I have some binding sites with ions, I
>> have
>> removed some ions from binding sites before pulling and In pulling
>> simulations have pullaed pulled the adjacent ions to the vacant binding
>> site (tunnel is aligned along  Y- axis).
>> for this I have used the following options in .mdp file.
>>     ; Pull code
>> pull            = umbrella
>> pull_geometry   = distance
>> pull_dim        = N Y N
>> pull_start      = yes
>> pull_ngroups    = 1
>> pull_group0     = REFA
>> pull_rate1      = 0.01
>> pull_k1         = 3000      ; kJ mol^-1 nm^-2
>>
>> Here  pull_group0 = REFA is the ion at another binding site and
>> pull_group1     = ATBP  is the atom  that I am pulling to the vacant site.
>> In next step I have performed umbrella sampling simulations to the
>> selected
>> configurations using the following options :
>> ; Pull code
>> pull            = umbrella
>> pull_geometry   = distance  ; simple distance increase
>> pull_dim        = N Y N
>> pull_start      = yes       ; define initial COM distance > 0
>> pull_ngroups    = 1
>> pull_group0     = REFA
>> pull_group1     = ATBP
>> pull_init1      = 0
>> pull_rate1      = 0.0      ; 0.01 nm per ps = 10 nm per ns
>> pull_k1         = 3000      ; kJ mol^-1 nm^-2
>> pull_nstxout    = 100
>> pull_nstfout    = 100
>> After that I have constructed PMF profile using Gromacs tool "g_wham",
>> while using g_wham I am getting the following warnings,
>> "WARNING, no data point in bin 34 (z=0.889382) !
>> You may not get a reasonable profile. Check your histograms!"
>> I have checked my histograms instead of one histogram for each
>> configuration with perfect overlapping, I am getting only one histogram.
>>
>
> You're probably just plotting the file wrong.
>
> xmgrace -nxy histo.xvg
>
>
>  Here I am sending the link that containing PMF profile and histogram that
>> have obtained.
>> http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpg<http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg>
>> http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpg<http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg>
>>
>>
> The PMF suggests massive undersampling (or complete lack of sampling) in
> several areas.
>
>
>  the weired thing that I have observed in my pulling simulations is that I
>> have expected motion of ion in positive Y-direction for my pull parameters
>> but it is moving in negative Y- direction.
>>   Can anybody please suggest me a solution for this,  Am I following
>> correct
>> protocol to get PMF of my system, is there any better method that suits
>> for
>> my system.
>>
>>
> If you are trying to see a complete translocation of an ion through a
> channel, the "distance" geometry is inappropriate, as it does not deal
> correctly with the change of sign for the vector between the reference and
> pulled group, IIRC.  Try "position" geometry and associated settings.
>
> -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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