[gmx-users] problem in running gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 21 11:33:22 CET 2009

nitu sharma wrote:
> Dear all ,
>                     I have successfully installed gromacs on my "32 bit 
> i686 fedora core linux system" but the problem is when I put the command 
> "mdrun " it gives out put like this
>  :-)  G  R  O  M  A  C  S  (-:
>                Giant Rising Ordinary Mutants for A Clerical Setup
>                             :-)  VERSION 3.3.2  (-:
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2007, 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.
>                                 :-)  mdrun  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s      topol.tpr  Input        Generic run input: tpr tpb tpa xml
>   -o       traj.trr  Output       Full precision trajectory: trr trj
>   -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr 
> format)
>   -c    confout.gro  Output       Generic structure: gro g96 pdb xml
>   -e       ener.edr  Output       Generic energy: edr ene
>   -g         md.log  Output       Log file
> -dgdl      dgdl.xvg  Output, Opt. xvgr/xmgr file
> -field    field.xvg  Output, Opt. xvgr/xmgr file
> -table    table.xvg  Input, Opt.  xvgr/xmgr file
> -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> -rerun    rerun.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro 
> g96 pdb
> -tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
>  -ei        sam.edi  Input, Opt.  ED sampling input
>  -eo        sam.edo  Output, Opt. ED sampling output
>   -j       wham.gct  Input, Opt.  General coupling stuff
>  -jo        bam.gct  Output, Opt. General coupling stuff
> -ffout      gct.xvg  Output, Opt. xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
>  -pi       pull.ppa  Input, Opt.  Pull parameters
>  -po    pullout.ppa  Output, Opt. Pull parameters
>  -pd       pull.pdo  Output, Opt. Pull data output
>  -pn       pull.ndx  Input, Opt.  Index file
> -mtx         nm.mtx  Output, Opt. Hessian matrix
>  -dn     dipole.ndx  Output, Opt. Index file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    19      Set the nicelevel
> -deffnm      string         Set the default filename for all file options
> -[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
>                             xvg files for the xmgrace program
> -np          int    1       Number of nodes, must be the same as used for
>                             grompp
> -nt          int    1       Number of threads to start on each node
> -[no]v       bool   no      Be loud and noisy
> -[no]compact bool   yes     Write a compact log file
> -[no]sepdvdl bool   no      Write separate V and dVdl terms for each
>                             interaction type and node to the log file(s)
> -[no]multi   bool   no      Do multiple simulations in parallel (only with
>                             -np > 1)
> -replex      int    0       Attempt replica exchange every # steps
> -reseed      int    -1      Seed for replica exchange, -1 is generate a seed
> -[no]glas    bool   no      Do glass simulation with special long range
>                             corrections
> -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
>                             bombardment on your system
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: gmxfio.c, line: 706
> Can not open file:
> topol.tpr
> -------------------------------------------------------
> "Rub It Right Accross Your Eyes" (F. Zappa)
> Because  I am not expert in linux so I can't  understand what does this 
> output mean is it working properly or not and I also want to know about  
> "can not open file topol.tpr".
> If anyone has idea about this problem could you please let me know .

This is normal operation. There are default filenames for all the 
different files you might offer as input to all GROMACS programs. If the 
program can't find such a file to open it, then you get the above 
message, since such a file is required input.


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