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

[Tsjerk Wassenaar]

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