[gmx-users] area per lipid

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 29 04:25:56 CEST 2008

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.


> Please help
> Pragya Chohan
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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