Hi,<br><br>Thanks for the reply!<br><br>I tried the rates, and only the terminal with positive rate gets pulled.<br><br>The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything?<br>
<br>Thanks,<br>Sai<br><br><br><br><div class="gmail_quote">On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>
<br>
Sai Janani Ganesan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. <br>
I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein<br>
I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled.<br>
I chose different references, I do have some success but I don't think it is the best way to do it.<br>
<br>
How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong?<br>
<br>
This is my pull code:<br>
<br>
pull = umbrella<br>
pull_geometry = distance <br>
pull_dim = Y N N<br>
pull_start = yes pull_ngroups = 2<br>
pull_group0 = Chain-C<br>
pull_group1 = Chain-B<br>
pull_group2 = Chain-A<br>
<br>
%pull_vec1 = -31 0 0<br>
%pull_vec2 = 31 0 0<br>
</blockquote>
<br></div>
I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2 = 0.002 pull_k2 = 1000 <br>
</blockquote>
<br></div>
Here's the problem. You're telling the two pulled groups to move in the same direction. With "distance" geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br><div><br></div><i>"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr</i><br>