[gmx-users] Extreme

[Justin A. Lemkul]

pawan raghav wrote:
> Dear Justin,
>  
> Thanks for sharing your knowledge with me. I have gone through 
> the tutorial and observed -extrn extract projected structure along with
> first two eigen vectors. Each Eigen Vector represents minimum and 
> maximum strucuture value.
>  
> I am a bit confiused about the values for minimum and maximum. I dont 
> know the exact meaning of score for minmum and maximum values. Are these 
> values
>  deviation (Displacement) and what is its unit and which score is the 
> best score along any eigen vector?
>  
> Please help me out with this problem. Is it possible to extract minimum 
> energy sructructue from a MD trajectory by using G_anaeig. Give me some 
> clue about these minimum/maximum scores.Can i consider thhis mimimum or 
> maximum structure as a native structure?
>  

I thought this looked familiar.  You asked this question before:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053511.html

and received an answer with a very nice analogy:

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053517.html

I don't think there is any relationship in the maxima/minima to native 
structures.  If I recall, the extremes are based on an average structure, which 
may or may not actually have any physical relevance:

http://www.gromacs.org/Documentation/Terminology/Average_Structure

I doubt that g_anaeig is appropriate for determining any sort of minimum energy 
structure, but I have not used it extensively to know for sure.

-Justin

> Pawan Raghav
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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