[gmx-users] g_order 4.0.7
jayeetaedu at hotmail.com
Thu Mar 11 21:34:59 CET 2010
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.
The result does not change with -o or -od option. I have 128 lipids (not exactly dppc though, head group is different) and water.
> 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?
> > 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
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