[gmx-users] what factors effetc the simulation during energy minimization

[Justin A. Lemkul]

bhargavi ch wrote:
> hi..
>  
> the sudden shoot up was observed in the RMS because of molecule breakage 
> into monomer and dimer.we  have also mutated some surface hydrophobic 
> aminoacid  and dint observe shoot up in any of the mutation. We have 
> also observed the same shoot in the case of X ray crystallographic 
> structure of template protein, when we did 10 ps simulation. what are 
> the parameters which we need to take to avoid such shoot up??
>  

As Mark pointed out, based on your original description, you are probably seeing 
PBC effects.  Use trjconv to remove periodicity, and analyze the RMSD again.

-Justin

> thanx
> Bhargavi
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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