Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 31 19:22:30 CET 2008
> Thanks Justin for your response just glance below
> >> 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?
> I am considering only z-axis but I am plotting these values on X-axis in
OK. That makes sense now; I probably should have seen that the first time.
> >Your output also depends on what you've analyzed. Was it the bilayer
> as a whole? Just acyl chains? Headgroups?
> I am calculating density of Head groups, choline, water and system
> separately later all these including in a single graph.
> what is "M" shape peak refers?
No clue. What line does it correspond to in the plot? All g_density is
measuring is the density of a given group at a certain coordinate; I don't know
what else you are really after.
> Could clear my doubt.
> Thanks in advance.
> >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
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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