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">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>
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<br>
Hi Vivek,<br>
<br>
I explained related matters in some detail on this list earlier, and<br>
would urge not to use a structure other than the average for<br>
determining the components.<br>
<br>
The results on the cosine contents can be illustrated as follows:<br>
<br>
I. Using average<br>
<br>
Imagine you're moving from place A to place B. The principal component<br>
is B-A, and the average is (A+B)/2. Your score/projection is the<br>
position relative to the average; negative on one side, positive on<br>
the other. This ends up being a straight line in one dimension, but in<br>
higher dimensions you'll get a nice half cosine.<br>
<br>
II. Using fixed reference<br>
<br>
Let's say your reference is A, then your component is still B-A, but<br>
your score/projection is now the distance from A. It starts out at<br>
zero and increases. In higher dimensional space, this would give a<br>
projection that starts out approximately linear and levels off at some<br>
point. These components are awkward, and very hard to interpret.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
<br>
On Wed, Oct 19, 2011 at 10:08 AM, vivek modi <<a href="mailto:modi.vivek2009@gmail.com">modi.vivek2009@gmail.com</a>> wrote:<br>
> Hi,<br>
><br>
> I am doing Essential Dynamics on a protein (150 residues). The simulation is<br>
> 100ns long and the RMSD becomes very stable after 25ns.<br>
> I have gone through the mailing list archives but could not find a precise<br>
> answer to the following question.<br>
><br>
> When I calculate the cosine content for the first PC by taking the average<br>
> structure for fitting using g_covar it gives a very high value ~.8.<br>
> But when I change the reference structure to the starting structure then I<br>
> get a cosine value ~.1.<br>
><br>
> I also repeated the same by dividing my trajectory into two equal halves but<br>
> the cosine value with average structure as a reference is always very high<br>
> while it is reasonably low with starting structure taken as reference.<br>
><br>
> My question is why the cosine content is dependent on the fitting<br>
> structure used in g_covar? And, especially, which structure is<br>
> recommended to use in Essential Dynamics analysis ?<br>
><br>
><br>
> Any help is appreciated.<br>
><br>
><br>
> Thanks a lot.<br>
><br>
><br>
> Regards,<br>
><br>
> Vivek Modi<br>
> Graduate Student,<br>
> IITK.<br>
><br>
> --<br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<br>
<br></blockquote></div><br>