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:[email protected]]
Inviato: venerdì 11 settembre 2009 14.05
A: '[email protected]'
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?
I'd guess you're confusing the mechanism that internally appends a
suitable integer to the filename by providing both -s and -deffnm.
Please try without the redundant -s argument and let us know if that
worked. If so, perhaps this bit of code needs a small fix.
Mark
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: [email protected]
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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