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 <bipinel...@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@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-requ...@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
