Did you try to remove the "_" from your file name?
On Sep 11, 2009, at 14:04, Anna Marabotti <[email protected]>
wrote:
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 laun
ch 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 particul
ar, I inserted the above command into a script that is used on the m
achine to launch the program in an interactive way, but GROMACS retu
rns 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 t
he 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: [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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