[gmx-users] Re: Insertion of assymetric protein in a lipid bilayer

[Graham Smith]

>> I had to delete a different number of lipids
>> on each side of the bilayer, due the asymetric shape
>> of my protein.
>> Would this be a problem for a reliable md simulation,

> No, no problem at all. People have already done that
> and it worked.

I also agree that it should be fine.
A reference where exactly this was done is 

"Setting up and optimization of membrane protein simulations"
Jose D. Faraldo-Gomez, Graham R. Smith and Mark S. P. Sansom
Eur. Biophys J (2002) 31:217-227

You've seen the code that we used? I recently put it on the 
www.gromacs.org/contributions/ page. 

-Graham 

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Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr