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

[Justin A. Lemkul]

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:

http://wiki.gromacs.org/index.php/make_ndx

-Justin

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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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