[gmx-users] ngmx (was: Problem with g_rdf)

Justin Lemkul jalemkul at vt.edu
Wed Feb 20 14:12:44 CET 2013

On 2/20/13 12:46 AM, Hector Manuel Manzanilla Granados wrote:
> Excuseme dear Dr. Tomas, forgiveme the boldness,
> I'm new with this, and I dont know who to address
> when I have a problem. My name is Hector, and  I'm
> tryng to install the gromacs software in my computer;
> I follewed all the steps in the online manual, however
> when I compile Gromacs with the instruction: ngmx, I receiveç
> the following sentence:

Please don't hijack existing threads with unrelated questions.  Start a new 
thread by sending a new mail to gmx-users at gromacs.org.

> :-)  G  R  O  M  A  C  S  (-:
>             Glycine aRginine prOline Methionine Alanine Cystine Serine
>                              :-)  VERSION 4.0.7  (-:
>        Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>         Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>               Copyright (c) 2001-2008, 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.
>                                   :-)  ngmx  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>    -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>    -s      topol.tpr  Input        Run input file: tpr tpb tpa
>    -n      index.ndx  Input, Opt.  Index file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -b           time   0       First frame (ps) to read from trajectory
> -e           time   0       Last frame (ps) to read from trajectory
> -dt          time   0       Only use frame when t MOD dt = first time (ps)
> -------------------------------------------------------
> Program ngmx, VERSION 4.0.7
> Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737
> Can not open file:
> topol.tpr
> -------------------------------------------------------
> "It's Calling Me to Break my Bonds, Again..." (Van der Graaf)
> I don't understand what to do with this, may be you can get me a hint,

You haven't provided any input for ngmx to use, so it's trying to use default 
file names for the required input.  You must supply suitable files that you want 
to visualize using -s and -f.  Please do some basic Gromacs tutorial material to 
get yourself used to a normal workflow, expected options for common commands, 
etc.  For what it's worth, there are far better visualization programs available 
(for free) that surpass ngmx in terms of features.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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