minnale wrote:
Hi all,
I have small doubt on g_density, The bilayer thickness can be
estimated by calculating density profile here I have calculated density
for different groups in lipid system by g_density command.
The POPC density profile x-axis(z-nm) vs y-axis(density), it looks "M"
shape what is it mean first high and second high peak exactly?
Which axis are you analyzing? "x-axis(z-nm)" makes no sense to me. Is your
bilayer in the x-y plane (the canonical view), or does it have some other
orientation?
Your output also depends on what you've analyzed. Was it the bilayer as a
whole? Just acyl chains? Headgroups?
Whatever it is that you've analyzed, the output corresponds to the density
(kg/m^3) of that species at that point along the box dimension.
My idea is based on literature survey first peak tells one half of the
bilayer density and other peaks tells remain half of the bilayer
density.am I right?
So you're saying that the overall bilayer density should be the sum of the two
peaks you're seeing? I guess the proper interpretation will depend on the
answers to the questions I've posed above.
-Justin
Any suggestions would be appreciated.
Thanks in adavance
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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