Dear all ,<br><br> 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<br>
<br> :-) G R O M A C S (-:<br><br> Giant Rising Ordinary Mutants for A Clerical Setup<br><br> :-) VERSION 3.3.2 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2007, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br>
<br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br><br> :-) mdrun (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br>
-s topol.tpr Input Generic run input: tpr tpb tpa xml<br> -o traj.trr Output Full precision trajectory: trr trj<br> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)<br>
-c confout.gro Output Generic structure: gro g96 pdb xml<br> -e ener.edr Output Generic energy: edr ene<br> -g md.log Output Log file<br>-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file<br>
-field field.xvg Output, Opt. xvgr/xmgr file<br>-table table.xvg Input, Opt. xvgr/xmgr file<br>-tablep tablep.xvg Input, Opt. xvgr/xmgr file<br>-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb<br>
-tpi tpi.xvg Output, Opt. xvgr/xmgr file<br> -ei sam.edi Input, Opt. ED sampling input<br> -eo sam.edo Output, Opt. ED sampling output<br> -j wham.gct Input, Opt. General coupling stuff<br>
-jo bam.gct Output, Opt. General coupling stuff<br>-ffout gct.xvg Output, Opt. xvgr/xmgr file<br>-devout deviatie.xvg Output, Opt. xvgr/xmgr file<br>-runav runaver.xvg Output, Opt. xvgr/xmgr file<br> -pi pull.ppa Input, Opt. Pull parameters<br>
-po pullout.ppa Output, Opt. Pull parameters<br> -pd pull.pdo Output, Opt. Pull data output<br> -pn pull.ndx Input, Opt. Index file<br>-mtx nm.mtx Output, Opt. Hessian matrix<br> -dn dipole.ndx Output, Opt. Index file<br>
<br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 19 Set the nicelevel<br>-deffnm string Set the default filename for all file options<br>
-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br>-np int 1 Number of nodes, must be the same as used for<br>
grompp<br>-nt int 1 Number of threads to start on each node<br>-[no]v bool no Be loud and noisy<br>-[no]compact bool yes Write a compact log file<br>-[no]sepdvdl bool no Write separate V and dVdl terms for each<br>
interaction type and node to the log file(s)<br>-[no]multi bool no Do multiple simulations in parallel (only with<br> -np > 1)<br>-replex int 0 Attempt replica exchange every # steps<br>
-reseed int -1 Seed for replica exchange, -1 is generate a seed<br>-[no]glas bool no Do glass simulation with special long range<br> corrections<br>-[no]ionize bool no Do a simulation including the effect of an X-Ray<br>
bombardment on your system<br><br><br>-------------------------------------------------------<br>Program mdrun, VERSION 3.3.2<br>Source code file: gmxfio.c, line: 706<br><br>Can not open file:<br>
topol.tpr<br>-------------------------------------------------------<br><br>"Rub It Right Accross Your Eyes" (F. Zappa)<br><br>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".<br>
If anyone has idea about this problem could you please let me know .<br><br>Thank you very much in advance.<br><br><br>Nitu Sharma<br><br>Structural biology lab<br>School Of life Sciences<br>Jawaherlal Nehru university<br>
new delhi, India.<br><br><br>