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. > >-Justin > >>Any suggestions would be appreciated. >> >>Thanks in adavance >> >> >> >>Black578x38_banner2.gif >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL >> PROTECTED]/2606998_2599290/2602379/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >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 > >========================================
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
