[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file?

[a a]

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: tsjerkw at gmail.com
> To: gmx-users at 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 <patd_2 at 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
> >
> >
> > --
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> 
> 
> -- 
> 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
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