[gmx-users] g_density?

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 31 19:22:30 CET 2008

```
minnale wrote:
> 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
> gnuplot.
>

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.

-Justin

> Could clear my doubt.
>
>
>  >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.
>  >>
>  >>
>  >>
>  >>
>  >>Black578x38_banner2.gif
>  >>
>  >>
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>  >-- ========================================
>  >
>  >Justin A. Lemkul
>  >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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>
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--
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Justin A. Lemkul