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

Anna Marabotti anna.marabotti at isa.cnr.it
Fri Sep 11 18:02:07 CEST 2009

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


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:




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.

So my question is: how does GROMACS “understand” that it has to interpret
“REMD_.tpr” not as a single file, but as a group of files indexed _0, _1, _2
and so on? Does it depend on the order of the options? Could you please give
me some hints about?


BTW, another problem: I tried to find solution searching in the
oldwww.gromacs.org site, but I am still unable to consult the gmx-users
archives using a keyword as it was possible in the past. How can I find
information in the GROMACS archives?


Many thanks and regards


Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make a difference, try sleeping with a
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