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.
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.
>
>-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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========================================
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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