Dear Tsjerk, Am I correct to say the cosine content of the first three principal components are as follows: PC1 : 0.602921 PC2: 0.011185 PC3: 0.0659901 As my coscont.xvg file is as follows: > > @ 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
Best regards, Catherine > Date: Tue, 10 Apr 2012 13:12:40 +0200 > Subject: Re: [gmx-users] How to extract the first three PC's cosine content > from the "coscont.xvg" file? > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > 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
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