[gmx-users] problems running REMD on grids
anna.marabotti at isa.cnr.it
Fri Sep 11 14:04:38 CEST 2009
I'm trying to perform some REMD calculations with GROMACS 4.0.5, and I found on the Wiki site these
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 mosquito"
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