[gmx-users] problem in running gromacs

nitu sharma sharmanitu35 at gmail.com
Sat Feb 21 10:06:03 CET 2009

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
  -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
-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
-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
-[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:

"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 .

Thank you very much in advance.

Nitu Sharma

Structural  biology lab
School Of life Sciences
Jawaherlal Nehru university
new delhi, India.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090221/e0e5ab41/attachment.html>

More information about the gromacs.org_gmx-users mailing list