[gmx-users] Re: Error in Membrane simulations with POPC bilayer
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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