[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 20:20:19 CEST 2012

On 10/2/12 2:16 PM, James Starlight wrote:
> Dear all!
> Recently I've forced with the same problem as was in this topic :)
> I have tieleman's lipids consisted of 128 dppc with water.
> also I have system with the protein inserted in the same bilayer
> I wounder to know
> 1- How I could change lipid number in the pure lipid bilayer (
> increase up to 200 lipids) with standard Gromacs tools ?
> I've tried use
> genbox -cs dppc128_whole.gro -box 8.04542  8.04542  10.19156
> where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045)
> As the consequence that prodyce larger system with increased amount of
> water in upper and lower layers but the lipid number was the same.

The proper approach is to set values for the box that are larger in x and y, but 
the same size in z.  That way, the new "solvation" occurs within the same plane 
as the membrane.

> 2- Is there any way to increase lipid number ( to add lipids from each
> size of the system) in the bilayer with the inserted protein ?

Using the same approach, with a slight modification:

genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z)

Increase the values of x and y, and leave z alone.



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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