[gmx-users] Regarding g_analyze

[Justin A. Lemkul]

bharat gupta wrote:
>  
> I generated this graph using xyplot since I was not able to install 
> xmgrace on windows platform .. also I want to one more thing ... that I 
> calculated the rmsd and rmsd_xtal graph .. I found them to be same and 
> the fluctuations in graph is same for 0 to 1.5 nm and then last  2.4 to 
> 3 ns .. does it mean that the structure is stable.. I have attached both 
> the files and the plotted file also.. pls if possible do comment on this 
> issue also..
> 

3 ns is fairly short to conclude that anything is truly stable.  Watch the 
trajectory to see what's going on.  I see nothing obviously wrong with either 
RMSD plot.

-Justin

> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
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> 

-- 
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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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