[gmx-users] Coordinate file for lipid bilayer
jalemkul at vt.edu
Tue Oct 2 21:01:40 CEST 2012
On 10/2/12 2:56 PM, James Starlight wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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