[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane

Parul tew parultew at gmail.com
Fri Jan 28 10:33:45 CET 2011

the protein I am working on is a very large transmembrane protein. I used
the DPPC bi layer membrane from peter teilman site and moved my protein into
the membrane using VMD.
the protein being very big is protruding out of the lipid membrane. Now I
want to solvate my whole protein for simulation studies.
I am following the Justin A lemkul tutorial KALP15 in DPPC in step 3 we have
to define the dimensions of the box to solvate the whole system. what could
be the How can I define the box so that my whole protein is inside the box.
In the tutorial as I understand in the editconf step we have to give the
membrane box vectors but if i will do so my protein will be out of the box.
That is to say I want to fill spc (water
) above and below the bilayer DPPC so that I have a fully solvated system.
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