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Hello again,<br>
<br>
You can use g_covar to extract the eigenvector of your choice and then
g_anaeig to extract only the motions along the desired eigenvector (use
g_anaeig -extr or g_anaeig -filt).<br>
<br>
make_edi creates an input file which you can use to run EDS or flooding
in gromacs, but from what you describe you don't want that.<br>
<br>
I'd also recommend reading the papers of Berk Hess from 2000 IIRC
regarding PCA of MD simulations. Analysing one eigenvector will not
always be meaningful.<br>
<br>
Good luck,<br>
Ran.<br>
<br>
Anirban Ghosh wrote:
<blockquote cite="mid372349.79075.qm@web8515.mail.in.yahoo.com"
type="cite">Hi All,<br>
I actually want to do the analysis in a particular direction of motion
i.e. along first principle component, thats why i am trying to run the
make_edi command, to get the desired direction component. <br>
Please suggest how to proceed to achieve this type of analysis.<br>
<br>
Regards,<br>
<br>
<br>
<div> </div>
<div><font color="#0000bf"><strong>Anirban Ghosh</strong></font></div>
<div><font color="#0000bf"><strong>M.Tech Bioinformatics</strong></font></div>
<div><font color="#0000bf"><strong>University of Hyderabad</strong></font></div>
<div><font color="#0000bf"><strong>Hyderabad - 500 046</strong></font></div>
<div><font color="#0000bf"><strong>Andhra Pradesh</strong></font></div>
<div><font color="#0000bf"><strong>India</strong></font></div>
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<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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