Membrane simulation

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Hai All,

I am working on a large protein of around 700 residues and I am using dppc 128 lipids as bilayer.
I changed the coordinates of the box such a way that the protein as a whole is inside the box. But on packing the lipids and shrinking (as in tutorial), a portion of the protein lies outside the box. How can this be solved ?

Should I change the lipids to POPC / POPE ?

2

In regard to the type of lipid, no that will not make a difference. However, you did not mention the inclusion of water. Is there any ? Many large proteins are trans-membrane and without water they will not behave correctly - neither will the membrane.

3

Thanks for the reply.
I could solve the issue by using translate command.