[gmx-users] Regarding cosine content

[bipin singh]

Thanks for the reply...
I calculated principal components per protein using the command
g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp
eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns
-extr extr.pdb -filt filt.xtc -first 1 -last 2

Also please suggest how one can differentiate between the two
scenarios, when the high cosine content is due to random diffusion or
conformational changes ?


On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Bipin,
>
> It seems one of the proteins is taking longer to reach an equilibrium.
> Maybe it is undergoing a conformational change?
> Did you calculate the principal components per protein, or for the
> joint trajectories? It would have been better to echo the commands you
> used on the list, because it might result in a different
> interpretation. I also made some comments on the list a short while
> ago regarding the interpretation of projections and cosine content.
> Maybe they can help you form a picture of what is happening :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh <bipinelmat at gmail.com> wrote:
>> Hello all,
>>
>> I have done PCA from 50ns long trajectory for two similar proteins
>> (length 180 aa and RMSD 0.2 A).
>> The equilibration time and final simulation condition were identical
>> for both the protein.
>> But when I checked the cosine content for PC1 for both proteins they
>> were 0.9 and 0.5 respectively.
>> What can be the reason for this huge difference in cosine content of
>> the two proteins ?
>>
>>
>> --
>> -----------------------
>> Regards,
>> Bipin Singh
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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--
-----------------------
Regards,
Bipin Singh



-- 
-----------------------
Regards,
Bipin Singh