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

Justin Lemkul jalemkul at vt.edu
Thu Oct 11 12:51:47 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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