[gmx-users] General Questions abdout gromacs

[Peter C. Lai]

You can also use the screen(1) command which makes the tty detachable.
http://www.gnu.org/software/screen/

On Tue, Nov 22, 2005 at 09:07:14AM +0200, Cesar Araujo wrote:
> 
> Hi,
> 
> I was using "nohup" command. With it the applications run at a little bit lower
> priority than normal but SIGHUP signals are ignored, so you can close safely
> your ssh or xterm sessions while your mdrun instance are still running. 
> 
> This is the syntax:
> 
> > nohup mdrun <your args> &
> 
> All the stdout output is automatically redirected to nohup.out text file.
> Perhaps you can redirect your stderr too, but also you should check the log
> files for error or warning messages.
> 
> Regards,
> C?sar.-
> 
> 
> Message: 1
> Date: Mon, 21 Nov 2005 20:55:01 +0200
> From: Itamar Kass <ikass at cc.huji.ac.il>
> Subject: Re: [gmx-users] General Questions abdout gromacs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1132599301.438218059058e at webmail.huji.ac.il>
> Content-Type: text/plain; charset=windows-1255
> 
> 
> Shalom Sven,
> 
> I use "mdrun -v -s ... & > logfile.md &" such all the output from the mdrun is
> being writen to a file. About using top, it might happen that gromacs had
> finished befor you checked.
> 
> Cheers, Itamar.
> 
> Quoting Sven Huttenhouse <mdsimulation at hotmail.com>:
> 
> >
> >
> > Thank you Dr. Erik
> >
> > I used the following command:
> > mdrun -nive 0 -v -s ............ ener.edr &
> > and then I closed the x window I used and re opened it again. I tried to see
> > what programs are running in the cluster using top but I didn't find the
> > mdrun running.
> >
> > did I used the right command? should there be a space between ".edr" and
> > "&"?
> > any suggestion??
> >
> >
> > kind regards
> > Sven
> >
> > >From: Erik Lindahl <lindahl at sbc.su.se>
> > >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > >Subject: Re: [gmx-users] General Questions abdout gromacs
> > >Date: Mon, 21 Nov 2005 19:33:44 +0100
> > >
> > >Hi Sven,
> > >
> > >On Nov 21, 2005, at 6:11 PM, Sven Huttenhouse wrote:
> > >
> > >>
> > >>Thank you all for replying
> > >>
> > >>What is the command that I have to use to run the mdrun in the  backgroun?
> > >
> > >Personally, I like the free program "GNU screen" that you can compile  if
> > >it isn't already installed. This gives you access to multiple  virtual
> > >terminals that can be detached and later reattached to see  the output.
> > >
> > >Alternatively you can just use "&" at the end of a command to run it  in
> > >the background.
> > >
> > >>where can I learn (read more) about  LINCS or SHAKE??
> > >>
> > >
> > >See the manual. Gromacs constraints use LINCS by default.
> > >
> > >Cheers,
> > >
> > >Erik
> > >
> > >-----------------------------------------------------------
> > >Erik Lindahl  <lindahl at sbc.su.se>
> > >Assistant Professor, Stockholm Bioinformatics Center
> > >Stockholm University, SE 106 91 Stockholm
> > >Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
> > >
> > >
> > >
> > >
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> 
> 
> 
> 
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585194
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
> 
> ----------------------------------------------------------------
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> 
> -- 
> Cesar Araujo, Lic. of Chemistry
> Department of Molecular Endocrynology
> Oulu University Hospital
> FIN-90029 OYS, FINLAND
> 
> phone: +358 8 3155632
> e-mail: cesar.araujo at oulu.fi
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-- 
Peter C. Lai
Dept. of Neurobiology
Yale University School of Medicine
http://cowbert.2y.net/