[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 21:01:40 CEST 2012

On 10/2/12 2:56 PM, James Starlight wrote:
> Justin,
> I've done exactly like you provide me ( changing only x and y )
> but in that case the protein and the old lipids were slightly shifted
> to one side of the new system. Is there any way to center the old
> system in respect to the new solvent ?

Define a new box and center with editconf -c -box.

> Also I've noticed that when I increase size of my system in x and y
> dimensions both of the water layers were increased greatly than lipid
> layer ( it's look like sandwich with two big bread pieces and smaller
> cutlet between them :) )

This suggests that something is wrong with the z-dimension.  I only say that 
because you had a 10-nm z-length in your previous post with the Tieleman DPPC 
bilayer, which is far larger than the coordinate file normally has.  genbox 
works by tiling the solvent coordinates through the empty space in the solute 
configuration.  If you're expanding in 3 dimensions, you can expect weird things 
to happen with membrane systems.



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


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