<br><br><div class="gmail_quote"><div>Hi Tsjerk,<br><br>Thanks for your earlier reply. It makes things clear.<br><br>Is it possible that the cosine content of first PC is high because of the fluctuations in the long loop regions which dominate and not in the secondary structures. The fluctuations in the loop regions is of no interest to me and I suspect it is making the cosine content high. If I repeat the calculations by selecting only the secondary structures (helices in this protein) and ignoring the loop regions, then the cosine content is fairly low. As I have a good understanding of the system I am working on I know that loops do not play any role. <br>
<br>Is it appropriate then to perform PCA by selecting only the secondary structure elements and not loops. What do you suggest ?<br><br><br>Regards,<br><br>-Vivek<br><br><br><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Message: 2<br>
Date: Thu, 20 Oct 2011 18:22:53 +0200<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Re: Re: Reference structure for g_covar<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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<CABzE1ShsV23CdH6vRDLe1NNAy-fbC1V+z+0ErwnF9heSebF7=<a href="mailto:w@mail.gmail.com">w@mail.gmail.com</a>><br>
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<br>
Hi Vivek,<br>
<br>
The high cosine content of the first pc indicates that the system is still<br>
equilibrating. You're sort of still on the road from A (the starting<br>
position) to B (the equilibrated state).<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
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<br>
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<br>
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<br>
other PCs the cosine content is very low.<br>
<br>
The question is that is it appropriate to ignore the first PC and make<br>
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>
Date: Wed, 19 Oct 2011 13:58:00 +0200<br>
> From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">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">gmx-users@gromacs.org</a>><br>
> Message-ID:<br>
> <CABzE1SjU=<a href="mailto:n78nWo%2Bo0utM7oVdWz4HbGjeyLj8x0NbweWWLzXiw@mail.gmail.com">n78nWo+o0utM7oVdWz4HbGjeyLj8x0NbweWWLzXiw@mail.gmail.com</a><br>
> ><br>
> Content-Type: text/plain; charset=ISO-8859-1<br>
><br>
> > > Hi Vivek, > > I explained related matters in some detail on this list<br>
> earlier, and > would urge...<br>
><br>
<br>
<br>
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