[gmx-users] Re: gmx-users Digest, Vol 41, Issue 15

[Ran Friedman]

Hello again,

You can use g_covar to extract the eigenvector of your choice and then
g_anaeig to extract only the motions along the desired eigenvector (use
g_anaeig -extr or g_anaeig -filt).

make_edi creates an input file which you can use to run EDS or flooding
in gromacs, but from what you describe you don't want that.

I'd also recommend reading the papers of Berk Hess from 2000 IIRC
regarding PCA of MD simulations. Analysing one eigenvector will not
always be meaningful.

Good luck,
Ran.

Anirban Ghosh wrote:
> Hi All,
> I actually want to do the analysis in a particular direction of motion
> i.e. along first principle component, thats why i am trying to run the
> make_edi command, to get the desired direction component.
> Please suggest how to proceed to achieve this type of analysis.
>
> Regards,
>
>
>  
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
> *Hyderabad - 500 046*
> *Andhra Pradesh*
> *India*
>
> ------------------------------------------------------------------------
> Try the revolutionary next-gen Yahoo! Mail. Click here.
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-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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