[gmx-users] area per lipid

Kukol, Andreas a.kukol at herts.ac.uk
Tue Apr 29 10:44:02 CEST 2008


First note that 0.658 is in nm^2 per lipid, while you quoted the box dimensions in Angstrom.

If you include the standard error of 0.009 nm^2, you will see that box size of the snapshot is within the error margin. The standard error is the sample standard deviation divided by sqr(N), with N = number of observations. That means individual snapshots can deviate even more from the average than the standard error would imply.

Hope this is helpful/


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of pragya chohan
Sent: 29 April 2008 05:08
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] area per lipid


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/
> ========================================
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