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

[Mark Abraham]

Anna Marabotti wrote:
> 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? 

-deffnm takes care of it. If you supply no -s filename, there's a 
default name, which you can change. REMD then manipulates that. You 
should have tried the command below and seen whether it works :-)

mdrun_mpi -np 16 -multi 16 -replex 1000 -deffnm REMD_

Mark

> 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.
> regards
> Anna
> 
> ----------------------------------------------------------------------
> 
> 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>  
> 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 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
> 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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