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: [email protected]
> To: [email protected]
> 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
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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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