[gmx-users] g_order 4.0.7

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 11 21:14:41 CET 2010

Jayeeta Ghosh wrote:
> Dear Gromacs Users,
> I am having similar problem that was reported by Sarah about a year ago. 
> I am using Gromacs4.0.7. I am using the following command to make the 
> index file.

It would be more efficient if you posted a link to the report of the issue.  If 
it is the problem I am thinking of, the output was not generated because of an 
incorrect index file, which may or may not be the case here.

> make_ndx -f dppc128.gro -o sn1.ndx
>  > a C34
>  > a C36
>  > ...
>  > a C50
>  > del 0-2
>  > q
> I am using following command to calculate the order parameter.
> g_order -n sn1.ndx -od 
> I am using all other default input file names. I am only getting two 
> output files: sg-ang.xvg and sk-dist.xvg, no order.xvg.
> I am not sure how to get around this.

That's very weird, the files you're getting are the optional output, which you 
haven't specified.  If you add -o and -od (for both order.xvg and deuter.xvg), 
is the result any different?  Does your system indeed contain only lipids?


> I would really appreciate any help.
> Thanks,
> Jayeeta
> // 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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