[gmx-users] problem in running gromacs

[Tsjerk Wassenaar]

Hi,

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.

Cheers,

Tsjerk

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