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 <tsje...@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 <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 > -- ----------------------- 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