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

[minnale]

Thanks for Reply, 
I am using 310k T for POPC Bilayer.I have found area per lipid 0.63nm^2/sec at 310k in gmx-archives. I have got the value 0.64522nm^2/sec and asked to gmx-archvies people replied, that is reasonable value.
the reference value is right?
Thanks in advance

On Sat, 14 Jun 2008 Jojart Balazs wrote :
>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?
>Balazs
>
>
>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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