[gmx-users] Lipid Order Parameters - Calculating & Plotting

[Alan Dodd]

Check previous questions to the mailing list:

http://www.gromacs.org/pipermail/gmx-users/2002-January/000527.html

http://www.gromacs.org/pipermail/gmx-users/2004-February/009182.html



--- Arneh Babakhani <ababakha at mccammon.ucsd.edu>
wrote:

> Hello GROMACS community,
> 
> I was wondering if somebody could walk me through
> the process of
> calculating lipid order parameters (for a DMPC
> membrane), using the
> g_order analysis tool?
> 
> I've got a 5 ns trajectory and would like to make
> one of the classic
> order parameter plots:
> i.e.
> On the y-axis: the order parameter averaged over the
> entire trajectory
> On the x-axis: the Carbon number, or Carbon type
> (C2A on one tick, C2B
> on the next tick, and so on . . . ).
> 
> I'm a little confused in how to set up the ndx file
> for this too.
> 
> Any help at all would be much appreciated!
> 
> Thank you for your time,
> 
> Arneh
> 
> 
> 
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