[gmx-users] Understanding the concept of area per lipid calculation

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jun 15 06:57:55 CEST 2008

minnale wrote:
> Hi all,
>     this may be a trivial query to you. I want to calculate the area of 
> lipid molecule. I have searched in gmx-archives and found how calculate 
> the area of lipid molecule with respective Time(ps). I would like to ask 
> two questions
> 1. Why we are concerning about (Box-x * Box-y)/(lipids of monolayer), 
> why cant Box-z?

Because by convention the Z direction is orthogonal to the lipid surface.

> 2. Box-x and Box-y means length of simulation box, if we increase the 
> length of box sizes in x,y and zaxes for the system with 200 lipids(both 
> sides) in that case is it possible to get simulation value near to 
> experimental value 0.63nm^2/sec for POPC.

What useful equilibrium quantity has dimensions of length^2 per unit time?


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