[gmx-users] General Questions abdout gromacs

[Itamar Kass]

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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