[gmx-users] RDF output has no data

[Venkat Reddy]

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.
> >
> >
> > On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy <venkat4bt at gmail.com>
> > wrote:
> > >
> > > > Dear users
> > > >
> > > > I have used AMBER MD package to run simulation for a solvent box. I
> am
> > > now
> > > > using the gromacs utility to calculate rdf as follows:
> > > >
> > > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
> > > >
> > > > However, I get no data in the output rdf.xvg. Since Im using
> specially
> > > > generated force field parameters, I do not know how to go about
> > > generating
> > > > a tpr file (in case that is the problem). The rdf.ndx file is correct
> > for
> > > > my atom selection. Please suggest how to go about solving this.
> > > >
> > > >
> > > Blank output usually indicates the command failed, which should have
> been
> > > preceded by a rather obvious fatal error. If a .tpr file is required,
> > g_rdf
> > > will tell you (again, a fatal error).
> > >
> > > -Justin
> > >
> > > --
> > >
> > > ========================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540)
> > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
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> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036