[gmx-users] g_order 4.0.7

[Justin A. Lemkul]

Jayeeta Ghosh wrote:
> I am sorry that I did not post the link to the report. I found that 
> sometimes these links do not work specially if they are too old.

Odd, I've never had that happen, even with the oldest of posts.  Regardless, 
always put your problem in context.

> http://lists.gromacs.org/pipermail/gmx-users/2009-March/040068.html
>  

Note that your problem is not entirely the same.  The reported issue was with 
version 4.0, and the problem was not that the wrong output files were generated, 
it was that the desired output files were generated, but were empty.  This was 
not the result of a bug, it was an incorrect .ndx file being supplied to g_order.

> The result does not change with -o or -od option. I have 128 lipids (not 
> exactly dppc though, head group is different) and water.
> 

Does g_order print anything useful to the screen?  Usually it will warn about 
index file corruption if it has been created incorrectly.  Is there anything 
written to the (undesired) output files?  If your head groups are different from 
DPPC, are all the subsequent atom names the same?  What you posted earlier 
corresponds to naming specifically for the DPPC sn-1 chain; if your atom names 
and numbering deviates from that, it surely won't work.

I have analyzed a DPPC membrane using g_order, version 4.0.7, and can attest 
that it gives the proper output, so I don't think this is a bug.

-Justin

> Thanks much.
> Jayeeta 
>  > Date: Thu, 11 Mar 2010 15:14:41 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] g_order 4.0.7
>  >
>  >
>  >
>  > 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?
>  >
>  > -Justin
>  >
>  > > I would really appreciate any help.
>  > > Thanks,
>  > > Jayeeta
>  > > //
>  > >
>  > > 
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>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > 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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-- 
========================================

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

========================================