Re: 回复： Re: 回复： Re: [gmx-users] 2D projection and corresponding conformation

[Tsjerk Wassenaar]

Xi Zhao,

If you know these steps are normal, how come you don't know how to go
about? A projection on the plane spanned by two eigenvectors is the
projection of your structure onto one of these eigenvectors plotted
against the projection of your structure on the other. Each structure,
and therefore each projection, is time indexed. You should get a table
of:

Time Projection1 Projection2

from which it's trivial to get the time of a certain projection in the
plane, and hence the conformation.

_Alternatively_ it is possible from only the projections and the
corresponding eigenvectors to reconstruct an unphysical structure, if
that is what you want. How to do that is simple if you understand
principal component analysis. If you don't know principal component
analysis, you should first read up about that, until you understand
what it is about... and then you will know how to get what you want
(and what it means).

Cheers,

Tsjerk


2008/6/12 xi zhao <zhaoxiitc2002 at yahoo.com.cn>:
> Dear sir:
> For example, I only simulated a protein, further,
> 1. using g_covar producing eigenvalue.xvg and eigenvec.trr for all  Ca atoms
>  2 using g_anaeig producing  2d projection.xvg
> 3 how to obtain corresponding corformation in 2d projection using trjconv?
> these steps are normal, can you give me some advise! ?
> Thank you very much!
>
> Mark Abraham <Mark.Abraham at anu.edu.au> 写道：
>
> xi zhao wrote:
>> Dear sir :
>> I also know these,but can you give some detail procedure for obtaining
>> the corresponding conformations? Thank you in advance!
>
> No, because you've told us no detail of your procedure to generate your
> eigensystem and to produce the (labeled) projected points. Once you've
> got that, it's probably just a matter of applying trjconv thoughtfully.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623