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

[Xavier Periole]

on 10/29/02 2:39 AM, Marc Maderi at maderi2 at yahoo.fr wrote:

> Hi!
> 
> I am new to gromacs and am currently setting up a
> system with a membrane-embedded protein.
> 
> In order to insert the protein into the bilayer I have
> deleted lipids molecule overlapping with the protein.
> However, during the insertion of the protein in the
> bilayer, 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,
> e.g. create distorsions in the bilayer? If yes, how
> does one usually proceed to avoid this?
> 
> Many thanks,
> 
> Marc

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

Xavier


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