[gmx-users] RDF output has no data
venkat4bt at gmail.com
Sat Apr 6 07:19:41 CEST 2013
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 ""
@ subtitle "O21-H2_&_CAT"
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
> > 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
> > 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
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With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
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