[gmx-users] problems running REMD on grids

[Anna Marabotti]

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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