[gmx-users] Averege structure

[Justin A. Lemkul]

pawan raghav wrote:
> I have done 15ns MD simulations at 300k temp for a protein finally 
> obtained an average structure from g_rmsf. so please tell me is output 
> average structure is a sampled structure? is there no need of remd or 
> sampling further because I got plateau in RMSD calculation at last?

Some useful information:

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

>  
> I have strongly energy minimize by first steepest second by conjugate 
> gradient of my protein after simulation was completed. I have got 81% 
> residues in core region of RC plot by using this energy minimization 
> method. I have also used SPDBv instead of former one method for EM but 
> got 91% core region residues. Which methods should I choose to get the 
> good model? what are the essential criteria for a good model?
>  

Energy minimization simply provides a reasonable starting structure for MD 
simulation.  Different methods can certainly produce different results; it's up 
to you to determine what the functional significance of these changes might be.

-Justin

> 
> 
> -- 
> Pawan
> 

-- 
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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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