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

[Anna Marabotti]

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.

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

____________________________________________________
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
mosquito"
 
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