[gmx-users] Problem in pullx file

[Aswathy]

On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Aswathy wrote:
>
>> Dear Gromacs users,
>>
>> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis.
>> Initially I pulled the ligand from extra to intracellular side of the
>> protein. The pull code used are given below.
>>
>> pull                     = umbrella
>> pull_geometry            = distance
>> pull_dim                 =  N N Y
>> pull_start               = yes
>> pull_nstxout             =  10
>> pull_nstfout             =  10
>> pull_ngroups             =  1
>> pull_group0              =  r_57
>> pull_group1              =  r_C1
>> pull_rate1               =  0.005
>> pull_k1                  =  1000
>>
>> here group0 is one residue at the extracellular region and r_C1 is the
>> side chain Carbon atom of the ligand.
>>
>> My question is , the total length of the channel is almost 40 Angstrom and
>> as per my knowledge, when we did the pulling the pullx file will give the
>> coordinate of the ligand through the channel.
>>
>
> Not quite.  Look at the data labels in the .xvg file.  The pullx file
> contains the coordinates (in all of the pull directions) for the reference
> group, and then the distance between the reference and the pull group along
> all pull axes.

I am still confused.   I have measured the distance between the reference
group(residue outside) to the other end of the channel. that is around
40Angstrom. if so, 1dz should give around 40 Angstrom? Because  once the
pulling completed,  the distance between group0 and group1 , should be equal
to the length of the channel.

Sorry that i am repeating the same query, i think I am still preconceived
about this. Otherwise could you please suggest some good tutorial for the
same . I will read that.



>
>  Even though ligand reaches the opposite end of the channel, in pullx file
>> I am getting around 19 Angstrom in total.
>>
>> Again I calculate the g_dist of the ligand and the center of the channel,
>> it shows around 40 Ang in total . Please find the links provided
>>
>>
> You're measuring two different things.  The pullx distance is given
> relative to your pull_group0, which you said is a residue on one side of the
> channel.  Then you're using g_dist to measure to the center of the channel.
>
>  Am I misunderstanding anything about the pullx file.
>>
>> Could you please suggest me where thing get wrong?
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en<
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en
>> >
>>
>>
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en<
>> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en
>> >
>>
>>
> For some reason these documents are inaccessible.  It is probably better to
> use a site like photobucket and post actual images.  Google is great, but
> not everyone has an account and I've also been told that their usage
> agreement is troubling, in that anything you upload to Google Docs becomes
> property of Google.  Not something I've looked into, but I don't ever post
> my research data there.
>
>

> -Justin
>
>
>> Thank you,
>> --
>> -Aswathy
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Aswathy
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