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

[Marc Maderi]

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

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