[gmx-users] Regarding cosine content

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 17 13:04:14 CET 2011

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,


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

More information about the gromacs.org_gmx-users mailing list