[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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



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