<br><br><div class="gmail_quote">On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Aswathy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Gromacs users,<br>
<br>
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.<br>
<br>
pull = umbrella<br>
pull_geometry = distance<br>
pull_dim = N N Y<br>
pull_start = yes<br>
pull_nstxout = 10<br>
pull_nstfout = 10<br>
pull_ngroups = 1<br>
pull_group0 = r_57<br>
pull_group1 = r_C1<br>
pull_rate1 = 0.005<br>
pull_k1 = 1000<br>
<br>
here group0 is one residue at the extracellular region and r_C1 is the side chain Carbon atom of the ligand.<br>
<br>
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.<br>
</blockquote>
<br></div>
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.</blockquote>
<div>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. <br>
<br>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.<br><br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Even though ligand reaches the opposite end of the channel, in pullx file I am getting around 19 Angstrom in total.<br>
<br>
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<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Am I misunderstanding anything about the pullx file.<br>
<br>
Could you please suggest me where thing get wrong?<br>
<br>
</div><a href="http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en" target="_blank">http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en</a> <<a href="http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en" target="_blank">http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en</a>><br>
<br>
<a href="http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en" target="_blank">http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en</a> <<a href="http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en" target="_blank">http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en</a>><br>
<br>
</blockquote>
<br>
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.<br>
<br></blockquote><div> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thank you,<br>
-- <br>
-Aswathy<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>