[gmx-users] area per lipid
pragyachohan at hotmail.com
Tue Apr 29 06:07:31 CEST 2008
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).
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.
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?
I want to show that the bilayer model satisfies all the experimental results before going further.
Any suggestion is welcome.
> Date: Mon, 28 Apr 2008 22:25:56 -0400> From: jalemkul at vt.edu> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] area per lipid> > Quoting pragya chohan <pragyachohan at hotmail.com>:> > >> > dear users> >> > I am trying to calculate area per lipid. I have downloaded the structure from> > http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.> >> > Earlier posts say that area per lipid can be calculated as box-x*box-y> > /#no.of lipids per monolayer. what I fail to understand is> > 64.841*63.993/64 is not equal to 0.658 +/- 0.009.> >> > the box-x and box-y are calculated from g_energy. Am I understanding> > something wrong?> > The reference for this particular lipid says that the _average_ area per> headgroup is 0.658 +/- 0.009, not that the ending structure of the simulation> will have exactly that area per lipid. There is definitely going to be some> fluctuation along the trajectory, and the last frame is just a snapshot.> > -Justin> > >> > Please help> >> > Pragya Chohan> > _________________________________________________________________> > Fashion Channel : Want to know what’s the latest in the fashion world ? You> > have it all here on MSN Fashion.> > http://lifestyle.in.msn.com/> > > > ========================================> > 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 gmx-users at gromacs.org> 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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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