[gmx-users] problem in running gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Feb 21 12:15:23 CET 2009


Hmm, once you manage to deal with that issue, you're in for a gmx_sumi
fatal error. What's the thing with version 3.3.2 these days?
You really should try to get another version of Gromacs before continuing.



On Sat, Feb 21, 2009 at 11:33 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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