[gmx-users] Re: Re: problems running REMD on grids

Berk Hess gmx3 at hotmail.com
Mon Sep 21 09:30:39 CEST 2009

> Date: Mon, 21 Sep 2009 09:11:24 +0200
> From: anna.marabotti at isa.cnr.it
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: Re: problems running REMD on grids
> Dear Mark,
> I passed your suggestion to omit the -s flag to the person who developed the
> scripts to launch GROMACS on the grid (I'm only a final user with no
> permission to modify the scripts). We made several trials and I don't know
> exactly all the modifications he applied during all trials (it's not exactly
> a script that I launch as an .exe file, the system is a bit more complex and
> I cannot see directly the commands). In the final version of the script I
> know that the flag -s was kept with the suggestion of adding only the name
> of the tpr files, without extension. Now it works.
> Anna
> Date: Sat, 19 Sep 2009 05:22:16 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: problems running REMD on grids
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AB3DDE8.8000201 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Anna Marabotti wrote:
> > Dear gmx-users,
> > after a lot of trial (and errors) I finally got my REMD simulation. The
> > problem was solved essentially when we avoided indicating the extension of
> > the .tpr files: i.e.
> > 
> > mdrun -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_  -np 16
> > did not work, whereas
> > 
> > mdrun -s REMD_ -multi 16 -replex 1000 -deffnm REMD_  -np 16
> > did work.

This is very strange.
Both command lines work fine for me.
BTW: note that mdrun has no option -np.

> This sounds tantamount to my suggested solution of omitting the -s 
> parameter entirely. Did you try that? Did it work?
> > I'm posting it to leave a trace in the gmx-users archive; I'd suggest to
> > correct accordingly the example in the part "Execution steps" at
> > http://oldwiki.gromacs.org/index.php/REMD
> Dallas Warren wrote that originally, but I'll update it if you'll 
> confirm the above.
> Mark
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