[gmx-users] g_rdf problem

avinash kumar avinashk.iit.kgp at gmail.com
Sun Nov 4 01:57:58 CET 2007

Dear all,
  I am having a problem in running some post analysis commands like g_rdf on
my computer . When my simulation is complete I type in the following command
to calculate the radial distribution function for the system " g_rdf -f
traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 " and the program gives a
message like this

:-)  G  R  O  M  A  C  S  (-:

             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  g_rdf  (-:
Select a reference group and 1 group
Opening library file /usr/share/gromacs/top/aminoacids.dat
Group     0 (      System) has   648 elements
Group     1 (         SOL) has   648 elements
Select a group: 1
Selected 1: 'SOL'
Select a group: 1
Selected 1: 'SOL'
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000

After displaying this line the program does nothing further . I checked for
the installation of g_rdf and found it to be installed . My simulation was
completed and for command like "trjconv" can read all the frames . Then why
is "g_rdf" command failing to read all the frames?

eagerly waiting for a reply.
Avinash Kumar
3rd year undergraduate
IIT Khragpur,India
Mechanical Engineering Department
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