SV: SV: SV: [gmx-users] g_order version 4.0.x

Sarah Witzke sawit02 at
Tue Mar 10 12:02:08 CET 2009

I have now made a new .ndx file as written in the wiki - and it works!!! :-)
Thank you very much for your time Justin, I think what had confused my was the way the .ndx file was made in 3.3.3 and then the previous threads about the "new way" to make .ndx file in gromacs 4.0.x
Anyway, I'm very happy now! Thanks again.

-----Original Message-----
From: gmx-users-bounces at on behalf of Justin A. Lemkul
Sent: Mon 09-03-2009 23:42
To: Gromacs Users' List
Subject: Re: SV: SV: SV: [gmx-users] g_order version 4.0.x

Justin A. Lemkul wrote:
> Sarah Witzke wrote:
>> My .xtc file is 219.41 ns and therefor I thought to just use the last 
>> ~100 ns where my molecules have diffused into the membrane.
>> I have just run g_order again whitout the -b option: the result is the 
>> same, no order parameters.
>> My index file consists of just one big group. In that groups are the 
>> carbon atoms of the two lipid chains (and the two carbonyl carbons) 
>> for each of my 128 lipids. When running g_order it reads the .ndx file 
>> like this: 
> That is your problem.  You need individual groups for each distinct 
> carbon along the chain.  For an example for proper creation of these 
> groups, see here:

*Edit* I have gone ahead and created a g_order page.  The information about how 
to create index groups seems to fit better there.  Please refer to the new 
g_order page:


> -Justin


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080

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