Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 31 18:51:45 CET 2008
> 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
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.
> Any suggestions would be appreciated.
> Thanks in adavance
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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