[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Oct 3 19:11:57 CEST 2012

On 10/3/12 12:38 PM, James Starlight wrote:
> Justin,
> thanks for advises.
> Finally how I could effectively reduce size of my system (in x and y )
> to the defined pbc box size ( see picture to the previous comment) ?
> I've noticed that increasing of x and y to the 12 nm I obtain ideal
> shape of the bilayer without miss-matches of the left and right sizes.
> But when I try to decrease dimensions of that system from 12 to 8 nm
> genbox -cs xz.gro -box 8.04542 8.04542 10.19156
> I've obtained the system with the broadered water layers again ( as in
> the picture which I've shown).

My advice is still the same - you need box vectors that are compatible with both 
a sensible water layer and membrane leaflets.



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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