<p>Hi Vivek,</p>
<p>The high cosine content of the first pc indicates that the system is still equilibrating. You're sort of still on the road from A (the starting position) to B (the equilibrated state).</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Oct 20, 2011 5:07 PM, "vivek modi" <<a href="mailto:modi.vivek2009@gmail.com">modi.vivek2009@gmail.com</a>> wrote:<br><br>Hi Tsjerk,<br><br>Thanks a lot for your reply. <br>But now I will ask a very naive question.<br>
<br>My study involves understanding the dynamics of a group of closely related proteins. All of them are simulated for a period of 100ns each.<br>
I have also analyzed the RMSD using g_rms for all of them and it becomes very stable after 20-30ns for all the proteins.<br>But when I do PCA I see high cosines (~0.8) for the first PC. For all the other PCs the cosine content is very low.<br>
<br>The question is that is it appropriate to ignore the first PC and make inference about the motion of the protein by using other PCs ?<br><br><br>Thanks a lot.<br><br><br>Regards,<br><br>-Vivek Modi<br><br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Date: Wed, 19 Oct 2011 13:58:00 +0200<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Reference structure for g_covar<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
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>
> Hi Vivek,
>
> I explained related matters in some detail on this list earlier, and
> would urge...</font></p></blockquote></div><br>
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