[gmx-users] Problem in pullx file

[Justin A. Lemkul]

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

I guess I still don't understand your setup.  Are you pulling a ligand through a 
a channel and then beyond the reference group, out into some solvent?  Or are 
you just pulling the length of the channel, such that the ligand never exits the 
channel.

If you're pulling through the entire channel and then out into the solvent, the 
sign of dZ is going to change.  It might help if you post the first few output 
lines of pullx.xvg (not the headers and stuff, the actual data), as well as the 
last few.  That way I can understand exactly what you're dealing with.

> 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.
> 

There is a pulling tutorial on the Gromacs website, but nothing that deals with 
what you're doing.  Tutorials are designed to generally guide the user through a 
larger procedure, not explain every small piece of analysis.

-Justin

> 
> 
> 
>         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=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>
>         <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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> 
> -- 
> 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

========================================