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
--
========================================
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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