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

[paloureiro at biof.ufrj.br]

> 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!
>

Hello, Arneh.

1)First of all, you have to build an index.ndx (using make_ndx - see  
manual)creating a group for each methylene and one for the methyl.
For instance, it will give [ C17 ], [ C18 ] ..., [ C29 ] groups, for  
one tail of DMPC.
2)The index.ndx has to contain only this groups - you will have to  
delete the others!
3)g_order -n index.ndx -od deuter.xvg will give you -Scd.

Regards.

Pedro.

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