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

Jojart Balazs jojartb at pharm.u-szeged.hu
Sat Jun 14 18:53:09 CEST 2008

Dear Minnale,
just a comment.
Are you sure, that the APL value of POPC is about 0.63nm^2? Because, as 
far as I know, at 303K the APL is about 0.683nm^2. (Structure of fully 
hydrated fluid phase lipid bilayers with monounsaturated chains - Nagle 
et al.). Which temperature did you used?

minnale írta:
> 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?
> 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.
> Thanks in advance.
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