[gmx-users] Re: RDF output has no data

[Venkat Reddy]

Sir

I loaded the trajectory. There doesn't seem to be anything wrong with it.
Have no clue whats going wrong

Thanks


On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> I believe the problem is in the way which you used to convert AMBER
> trajectory to the GROMACS trajectory....
>
> I would suggest to try gmxdump and see what your trajectory looks like. Oe
> maybe even better - try to visualize it in VMD to see if the format is
> correct.
>
> Dr. Vitaly Chaban
>
>
>
> Sir
> >
> > I was using an old version. Now I used 4.5.5, it still gives me the same
> > blank output file.
> >
> > Kindly suggest how to go about solving this
> >
> > Thanks
> >
> >
> > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy <venkat4bt at gmail.com>
> > wrote:
> > >
> > > > There was no fatal error preceding the output. After selecting the
> > groups
> > > > following are the output on the screen
> > > > Reading frame       1 time    0.100
> > > > Warning: can not make broken molecules whole without a run input
> file,
> > > >          don't worry, mdrun doesn't write broken molecules
> > > >
> > >
> > > This message is from a prehistoric version of g_rdf. Please get a new
> > one.
> > >
> > > Mark
> > >
> > >
> > > >
> > > > Reading frame    2000 time  200.000
> > > >
> > > >
> > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman)
> > > >
> > > > And the rdf.xvg file looks like this
> > > >
> > > > #This file was created Sat Apr  6 10:54:13 2013
> > > > # by the following command:
> > > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
> > > > #
> > > > # g_rdf is part of G R O M A C S:
> > > > #
> > > > # GROningen MAchine for Chemical Simulation
> > > > #
> > > > @    title "Radial Distribution"
> > > > @    xaxis  label "r"
> > > > @    yaxis  label ""
> > > > @TYPE xy
> > > > @ subtitle "O21-H2_&_CAT"
> > > >      0.001          1
> > > > ~
> > > >
> > > > Whats going wrong? Please help.
> >
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036