[gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane

[Justin Lemkul]

On 10/11/12 5:57 AM, Shima Arasteh wrote:
> I visualized the last output mdrun of KALP15-DPPC simulation, the secondary structure of protein is complete and it seems OK. Can I trust on it and not care about the visualization of system after inflategro?
>
>

That's probably a reasonable conclusion.  Sometimes visualization can be 
misleading.  What you should trust the most is the outcome of the EM during 
shrinking of InflateGRO and whether it generates sensible forces.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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