[gmx-users] Water Tutorial and g_rdf

Matt Thompson thompsma at jilau1.colorado.edu
Wed Sep 20 20:59:22 CEST 2006

Folks, I'm a newbie at GROMACS who is going through the tutorial
outlined here:


All is well (aside from the bd-temp warning at the grompp command) until
I try to analyze the system.  Namely when I run:

  g_rdf -n index

it seems to lockup.  Now, maybe it's supposed to take a while, I don't
know, but after 35 minutes of 100% CPU on a Pentium D (and no end in 
sight), I began to wonder.  When I run it, the output on screen is:

> g_rdf -n index
                          :-)  G  R  O  M  A  C  S  (-:

                        GRowing Old MAkes el Chrono Sweat

                             :-)  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
Group     0 (          OW) has   216 elements
There is one group in the index
There is one group in the index
Reading frame       0 time    0.000

After that point, it takes a proc and runs with it.  Now one thing I
noticed was that in the tutorial it says:

The program will ask you for how many groups you want the calculate the
RDF, answer 1

The program doesn't ask me.

FYI, I compiled the program using the gromacs-3.3-1.src.rpm spec file 
but altered to use the 3.3.1 sources.  I have the compilation log that I 
tee'd, but the lines involving g_rdf don't have any error attached.

Thank you for any help,
Matt Thompson

The mayfly lives only one day, and sometimes it rains. - Geo. Carlin
    Matt Thompson -- http://ucsub.colorado.edu/~thompsma/
    440 UCB, Boulder, CO  80309-0440
    JILA A510, 303-492-4662

More information about the gromacs.org_gmx-users mailing list