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Hi <BR>
<BR>
I have read the reference quoted there and they have given the time evolution of area per head-group to decrease and become constant near that value (including last snapshot). <BR>
<BR>
Is the way described in earlier post correct? According to what I have seen, the structure at peter tieleman's site also has dimensions around 62-63 angstoms and average area per lipid is qouted by them is also around the same.<BR>
<BR>
the value of box-x and box-y i got from g_energy is also fluctuating b/w 6.2-6.3 nm. I want to see time evolution of area per lipid?<BR>
<BR>
I want to show that the bilayer model satisfies all the experimental results before going further.<BR>
<BR>
Any suggestion is welcome.<BR>
<BR><BR>> Date: Mon, 28 Apr 2008 22:25:56 -0400<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] area per lipid<BR>> <BR>> Quoting pragya chohan <pragyachohan@hotmail.com>:<BR>> <BR>> ><BR>> > dear users<BR>> ><BR>> > I am trying to calculate area per lipid. I have downloaded the structure from<BR>> > http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.<BR>> ><BR>> > Earlier posts say that area per lipid can be calculated as box-x*box-y<BR>> > /#no.of lipids per monolayer. what I fail to understand is<BR>> > 64.841*63.993/64 is not equal to 0.658 +/- 0.009.<BR>> ><BR>> > the box-x and box-y are calculated from g_energy. Am I understanding<BR>> > something wrong?<BR>> <BR>> The reference for this particular lipid says that the _average_ area per<BR>> headgroup is 0.658 +/- 0.009, not that the ending structure of the simulation<BR>> will have exactly that area per lipid. There is definitely going to be some<BR>> fluctuation along the trajectory, and the last frame is just a snapshot.<BR>> <BR>> -Justin<BR>> <BR>> ><BR>> > Please help<BR>> ><BR>> > Pragya Chohan<BR>> > _________________________________________________________________<BR>> > Fashion Channel : Want to know what’s the latest in the fashion world ? You<BR>> > have it all here on MSN Fashion.<BR>> > http://lifestyle.in.msn.com/<BR>> <BR>> <BR>> <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>> <BR>> ========================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><br /><hr />Windows Live Spaces : Help your online world come to life, add 500 photos a month. <a href='http://home.services.spaces.live.com/' target='_new'>Try it!</a></body>
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