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

Anna Marabotti anna.marabotti at isa.cnr.it
Mon Sep 14 11:31:04 CEST 2009

Dear gmx-users,
thank you for your answers. Just to point out since the order of my and your
messages is quite a bit confusing:

1) the command I used for REMD calculation appears corrupted in my previous
message: to be more clear, I'm reporting it here again. It seems to me that
it is as suggested in the wiki page:

mdrun_mpi -np 16 -s REMD_.tpr -multi 16 -replex 1000 -deffnm REMD_

I'm trying to summarize here your suggestions, and to answer to all.

For Mark: I don't really understand why you are saying that the command -s
is redundant. I always used the -s option to provide the .tpr input file to
mdrun! How can I provide the .tpr file to mdrun without using -s? 

For Berk: sorry but I did not find your answer (if any). Could you please
repeat it?

For Xavier: thanks for suggestion. I added the "_" because it was suggested
in the Wiki page.

Finally, for Justin: thank you very much for the link to the search option.

Sorry for bothering you again, I'm waiting for your comments.


Message: 1
Date: Sat, 12 Sep 2009 11:07:18 +0200
From: XAvier Periole <x.periole at rug.nl>
Subject: Re: [gmx-users] problems running REMD on grids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <CC9E9AF0-0BD9-42A3-B81A-E51D4E47F021 at rug.nl>
Content-Type: text/plain; charset="utf-8"

Did you try to remove the "_" from your file name?

On Sep 11, 2009, at 14:04, Anna Marabotti <anna.marabotti at isa.cnr.it>  

> 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 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
>  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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