[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 11 12:37:04 CET 2011

James Starlight wrote:
> Justin,
> Could you tell me what difference in inflategro parameters ( cut-off for 
> lipid removing and scaling factors) should I make for insertion protein 
> in another bilayes in comparison tu tutorial ?

I've never made any changes; it's always worked just fine.

> Now I'm working with DMPC. I've inserted symmetrical alpha helices 
> protein in this bilayer but inflategro deleate 2 lipid from upper and 
> just 1  from lower layer. It's strange because I suppose that equal 
> bilayer molecules would be removed :o

The number of lipids that are removed will depend on the starting configuration 
of the membrane and thus where lipids are relative to the protein. 
Theoretically, a symmetrical protein should delete an equal number of lipids 
from each leaflet, if the geometry of the top and bottom leaflets is comparable. 
  Either try placing the protein at a different location to achieve equivalent 
removal or manually delete a lipid and be sure to equilibrate adequately.

> On Inflategro's sites I havenot found such specifity for above 
> parameters for different bilayers :(

The cutoffs specified are simple grid search parameters.  They do not 
necessarily need to be altered depending upon the lipid type.



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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