[gmx-users] Orientation of protein

[Justin Lemkul]

On 9/12/12 4:28 AM, Shima Arasteh wrote:
> Dear users,
>
> As a matter of fact I don't know the exact orientation of my protein. To insert a protein in a lipid bilayer, I need to set the orientation of protein and bilayer parallel to z-axis. I'd like to know if it is necessary for protein to be in z-direction exactly? Is it acceptable to set the protein's direction approximately?
>

If you simulate for sufficiently long, likely the protein will adopt a 
reasonable orientation, provided that whatever you start with isn't too terribly 
far from reality.  That depends, of course, on the protein and whether or not 
forces like tilting and hydrophobic mismatch will play a significant role in the 
dynamics.

-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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