[gmx-users] Coordinate file for lipid bilayer

James Starlight jmsstarlight at gmail.com
Tue Oct 2 22:12:18 CEST 2012

This is exactly what I've obtained


the same effect was also in case of intact tieleman's lipid bilayers (
the water layers were broader than lipid after resizing with genbox)


2012/10/2, Justin Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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