[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Justin Lemkul jalemkul at vt.edu
Mon Jul 23 12:45:37 CEST 2012

On 7/23/12 5:31 AM, J Peterson wrote:
> Hi Justin,
> Thanks for all your help to get me through membrane simulations.
> I've a problem to be solved. I need a long and thick membrane to simulate a
> big protein. The longest bilayer that I can download from Tieleman's website
> is 64 molecules long.
> How can I make (double or triple the bilayer) a long and thick bilayer to
> accommodate a large protein?
> Are there any experimental evidence about the thickness of the membrane that
> should be followed before expanding the membrane?

You can expand a membrane patch in the x-y plane using genconf -nbox.  That will 
give you a greater lateral size to work with.  I don't know what exactly you 
mean by making the membrane thicker.  Each lipid has an experimentally 
determined thickness (usually P-P distance) under given conditions (temperature, 
ionic strength, etc).  In physiological membranes, proteins will tilt or kink 
due to hydrophobic mismatch if their dimensions exceed that of the hydrophobic 
core.  If you need something that has a thicker hydrophobic core, then you may 
need to be looking into building your own membranes from scratch.



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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