[gmx-users] General Questions abdout gromacs

[Cesar Araujo]

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,
César.-


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
> >
> >
> >
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the www interface
> >or send it to gmx-users-request at gromacs.org.
>
> _________________________________________________________________
> Don’t just search. Find. Check out the new MSN Search!
> http://search.msn.click-url.com/go/onm00200636ave/direct/01/
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>




===========================================
| 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
============================================

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.


-- 
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