[gmx-users] R: problems running REMD on grids
gmx3 at hotmail.com
Fri Sep 11 19:03:54 CEST 2009
> Date: Sat, 12 Sep 2009 02:35:28 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] R: problems running REMD on grids
> Anna Marabotti wrote:
> > I'm re-sending the message below because it seems to me that it has not
> > arrived to the list.
> > Please forgive me in case of duplicate sending.
> > Best regards
> > Anna
> > _____
> > Da: Anna Marabotti [mailto:anna.marabotti at isa.cnr.it]
> > Inviato: venerdì 11 settembre 2009 14.05
> > A: 'gmx-users at gromacs.org'
> > Oggetto: problems running REMD on grids
> > Dear gmx-users,
> > I’m trying to perform some REMD calculations with GROMACS 4.0.5, and I found
> > on the Wiki site these instructions:
> > http://oldwiki.gromacs.org/index.php/REMD
> > that I’m trying to follow, but I encountered some problems.
> > If I understand well the instructions, if I want to perform replicas at N
> > different temperatures, I have to create N different .mdp files and then N
> > different .tpr files, that I should name “filename”_0, “filename”_1...
> > "filename”_N-1. That’s what I did: I created 16 different .mdp files and 16
> > .tpr files that I called REMD_0.tpr. REMD_1.tpr REMD_2.tpr ... REMD_15.tpr.
> > At this point, I have to launch the mdrun command with the –multi, -replex
> > (optionally, -reseed) options. Following the example in "Execution step", my
> > command line should be:
> > mdrun –s REMD_.tpr –multi 16 –replex 1000 –deffnm REMD_ -np 16
> > That's what I did, but I experienced some difficulties on the parallel
> > machines that I’m using to perform simulations. In particular, I inserted
> > the above command into a script that is used on the machine to launch the
> > program in an interactive way, but GROMACS returns an error saying that
> > “cannot open file REMD_.tpr” (and in fact, the file REMD_.tpr does not
> > exist, only files REMD_0.tpr, REMD_1.tpr etc do exist!) I also retried
> > launching the same command from the shell, but the error was the same
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