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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue May 30 07:04:05 CEST 2006

Hi Pedro, thank you for your prompt reply.

I'm attempting to do what you suggested.

1).  I create an index file, called sn2.ndx, which contains 14 groups, 
one group for each carbon type in the chain (labeled C2A, C2B, . . . C2N).

2)  I then try to execute the following command:
g_order -f FullMD10.trr -n sn2.ndx -s FullMD10.tpr -o order.xvg -od 
deuter.xvg -os sliced.xvg
(in accordance with your suggestion, and what's posted in the g_order 

I'm then asked to pick a group (from 0 to 13, corresponding to the 14 
carbon types that are in the index file).  So I assume then I have to 
calculate the Scd of each carbon, one at a time? That's fine, I can 
easily script that.

But when I pick a carbon, the following occurs:

Select a group: 0
Selected 0: 'C2A'
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#

Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
Last frame       1000 time 1000.000

gcq#195: "I Am a Poor Lonesome Cowboy" (Lucky Luke)

So the end result is a file called sg-ang.xvg and sk-dist.xvg.   Why 
didn't I get any of my output files (order.xvg, deuter.xvg, and 
sliced.xvg) ???

Thanks again,


paloureiro at biof.ufrj.br 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!
> 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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