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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Mon Jun 5 09:08:05 CEST 2006

The bug in g_order has been resolved, see:

Arneh Babakhani 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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