[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 21:55:31 CEST 2012

On 10/2/12 3:49 PM, James Starlight wrote:
> Justin
> Previously I've expanded initial system on Z-dim before the protein
> was inserted to increase both water layers.
> After current processing with Genbox there is no problems in Z
> actually- it look likes sandwich with two broader bread layers and
> narrower cutlet :) So the lipid layer in x and y is thinker than water
> ( so the lipid number stay the same after resizing).

Posting a link to an actual image would be really useful here.  I'm not sure I 
understand your metaphor exactly.

If you're looking to add lipids and water around an existing system, the 
z-dimension of the solute and solvent boxes have to be the same.  So if you have 
a system that you have extended in z to accommodate a protein or whatever else, 
you need to manipulate a DPPC-only system in the same way - extend its 
z-dimension to be the same as the "solute," maintaining the relative position of 
the membrane within the new "solvent" box, and then add water in the "solvent" 
configuration to fill that box.  Then proceed as I've suggested before.  It 
should be obvious from all of this that it is vastly easier to plan a box of 
sufficient size before starting ;)



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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