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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri May 26 19:37:13 CEST 2006

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:
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,


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