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

[Jojart Balazs]

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.
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> ------------------------------------------------------------------------
>
>
> No virus found in this incoming message.
> Checked by AVG. 
> Version: 8.0.100 / Virus Database: 270.3.0/1502 - Release Date: 13/06/2008 19:25
>