You could load your gro and trr file into vmd, label the angle, save the file and plot using excel.<br><br>Oly<br><br><div class="gmail_quote">On 28 April 2010 22:26, 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>
Nilesh Dhumal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
I am doing solvation of glucose. I am trying to calculate a angle between<br>
three selected carbon atoms.<br>
If I run g_angle using angle.ndx file it consider all carbon atom. In<br>
force field C-C-C 112.5 is specified so it’s making a group of all carbon<br>
atoms. I am interested in selected carbon atoms.<br>
How can I plot an angle of selected three carbon atoms?<br>
</blockquote>
<br></div>
Make an appropriate index group, which it doesn't sound like you've done. If there's a specific angle you want to measure, you don't even necessarily need make_ndx, just write the group using a text editor with the appropriate atom numbers.<br>
<br>
-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>
Thanks<br>
<br>
Nilesh<br>
<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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