[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Sat Oct 15 19:44:05 CEST 2011

James Starlight wrote:
> Dear Gromacs's users!
> I'd like to simulate some membrane proteins in their native environment.
> Recently I've found a good tutotial of the same simulation of the KALP 
> peptide in DPPC membrane 
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html).
> Is there  someone who have also tried to make thit tutorial ?

Yes, per our server logs, several hundred people have :)

> First of all its very intresting for me the positioning of the protein 
> in the membrane via specific  perl script called infrategro. What values 
> for the cutoff radius as well as measurements of  the area per lipid  
> are most adequate for different membrane proteins?

The ones given in the tutorial work quite well.  They are the defaults suggested 
by the developers of InflateGRO.

> Could you also tell me some alternative ways of full algorithm of the 
> protein insertion in the membrane?

Careful use of genbox (but will require significantly more equilibration as 
there will be large gaps), or g_membed.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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