[gmx-users] RDF output has no data

[Mark Abraham]

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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