[gmx-users] RDF output has no data

[Venkat Reddy]

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

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