Hi Catherine, A converged system will yield low cosine content. But that can't be turned around! I can think of a lot of lines that don't match well with a cosine, but that are inconsistent with convergence.
That said, the index in the .xvg file is the principal component index. So the projection on the first pc has a cosine content of 0.6. Cheers, Tsjerk On Tue, Apr 10, 2012 at 5:28 AM, a a <pat...@hotmail.com> wrote: > Dear Sir/Madam, > > I used the following steps to get the cosine content for my trajectories, > could you please kindly tell me how to interpret the results? > > /usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v > > /usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v > eigenvec.trr -proj > > /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8 > > In the final "coscont.xvg", I found the followings: > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > # This file was created Tue Apr 10 10:59:12 2012 > # by the following command: > # /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8 > # > # g_analyze_d is p art of G R O M A C S: > # > # Giant Rising Ordinary Mutants for A Clerical Setup > # > @ title "Cosine content" > @ xaxis label "set / half periods" > @ yaxis label "cosine content" > @TYPE xy > 1 0.602921 > 2 0.011185 > 3 0.0659901 > 4 0.425943 > 5 0.204306 > 6 0.439315 > 7 0.0288551 > 8 0.0830944 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > I read some literature quoted the first three PCs's cosine content, if > the cosine content close to zero, the trajectory is converged. > > How can I extract the first three PCs's cosine content from the above > "conscont.xvg" file? Please kindly help. > > Best regards, > > Catherine > > > -- > 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