Date: Mon, 21 Sep 2009 09:11:24 +0200
From: anna.marabo...@isa.cnr.it
To: gmx-users@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.abra...@anu.edu.au
Subject: Re: [gmx-users] Re: problems running REMD on grids
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4ab3dde8.8000...@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.
Berk
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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