[gmx-users] Problem in pullx file

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 4 13:01:34 CEST 2010

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.

> 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 


> Thank you,
> -- 
> -Aswathy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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