<P>
Thanks Justin for your response just glance below<BR>
<BR>
>> Hi all,<BR>
>> 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.<BR>
>><BR>
>> 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? <BR>
><BR>
>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?<BR>
<BR>
I am considering only z-axis but I am plotting these values on X-axis in gnuplot. <BR>
<BR>
>Your output also depends on what you've analyzed. Was it the bilayer as a whole? Just acyl chains? Headgroups? <BR>
<BR>
I am calculating density of Head groups, choline, water and system separately later all these including in a single graph.<BR>
<BR>
what is "M" shape peak refers? <BR>
<BR>
Could clear my doubt.<BR>
<BR>
Thanks in advance. <BR>
<BR>
>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.<BR>
><BR>
>>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?<BR>
>><BR>
><BR>
>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.<BR>
><BR>
>-Justin<BR>
><BR>
>>Any suggestions would be appreciated.<BR>
>><BR>
>>Thanks in adavance<BR>
>><BR>
>><BR>
>><BR>
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>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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