[gmx-users] g_density?

minnale minnale_gnos at rediffmail.com
Fri Oct 31 19:24:48 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 gnuplot.  

>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? 

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
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