[gmx-users] inversion of lipid bilayer with water in the centre

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 16 13:09:13 CEST 2010

ram bio wrote:
> Dear Gromacs Users,
>  I have a lipid bilayer with me and I would like to simulate a system
> by keeping the water molecules with proteins in it and lipid
> surrounding the water on both sides, can any body suggest me please...

If you place the bilayer at the "bottom" of the unit cell, and the protein in 
water "above" the bilayer, then you indeed have a protein that is bounded by the 
leaflets of the membrane through PBC.

If you want to render that in some way such that you have the protein sandwiched 
within the leaflets of the membrane, you can use trjconv -center to center the 
unit cell around the protein, or perhaps trjconv -trans.  For the purposes of 
actually running the simulation, though, the PBC takes care of your issue fairly 


> Thanks
> Ram


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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