[gmx-users] problem with mdrun performing replica exchange MD

[Xavier Periole]

On Fri, 23 Nov 2007 12:42:45 +0100
  "Xavier Periole" <X.Periole at rug.nl> wrote:
> 
> David is write, you need to rename the tpr files is the following cmd:

well, I believe David was right not write :))

> mpirun -np 8 mdrun_mpi -s XXX.tpr -replex 2500 -reseed -1 -multi 8
> 
> by
> 
> XXX0.tpr
> XXX1.ptr
> ...
> XXX7.tpr
> 
> 
>> This time I used the following command line:
>> 
>> mpirun -np 8 mdrun_mpi -s simul0.tpr -replex 2500 -reseed -1 -multi 8. 
>> 
>> I got the following error:
>> 
>> Program mdrun_mpi, VERSION 3.3.99_development_20070413
>> Source code file: gmxfio.c, line: 706
>> 
>> Can not open file:
>> simul0_md0.tpr
>> -------------------------------------------------------
>> 
>> "Don't Eat That Yellow Snow" (F. Zappa)
>> 
>> Error on node 0, will try to stop all the nodes
>> Halting parallel program mdrun_mpi on CPU 0 out of 8.
>> 
>> I could not understand this error because I do not have such a file: 
>>simul0_md0.tpr.
>> 
>> 
>> -----Original Message-----
>>From: "Berk Hess" <gmx3 at hotmail.com>
>> To: gmx-users at gromacs.org
>> Date: Fri, 23 Nov 2007 10:58:48 +0100
>> Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange 
>>MD
>> 
>> You need to supply the -np option.
>> In Gromacs 3.3 you don't need to set the -multi option,
>> and -multi does not take an argument.
>> If you use the CVS head branch, you need to set -np and -multi
>> both with an argument.
>> 
>> Berk.
>> 
>>>From: "OZGE ENGIN" <OZENGIN at KU.EDU.TR>
>>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>To: gmx-users at gromacs.org
>>>Subject: Re: RE: [gmx-users] problem with mdrun performing replica exchange 
>>>MD
>>>Date: Fri, 23 Nov 2007 11:44:47 +0200
>>>
>>>Hi Berk,
>>>
>>>I indicated the number of replicas with -multi option. In additon, I have 
>>>compiled Gromacs with MPI support.
>>>
>>>I used the following command line:
>>>
>>>mdrun -s simul0.tpr -multi 16 -reseed -1 -replex 2500
>>>
>>>-----Original Message-----
>>>From: "Berk Hess" <gmx3 at hotmail.com>
>>>To: gmx-users at gromacs.org
>>>Date: Fri, 23 Nov 2007 10:36:57 +0100
>>>Subject: RE: [gmx-users] problem with mdrun performing replica exchange MD
>>>
>>>
>>>
>>>
>>> >From: "OZGE ENGIN" <OZENGIN at KU.EDU.TR>
>>> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >To: gmx-users at gromacs.org
>>> >Subject: [gmx-users] problem with mdrun performing replica exchange MD
>>> >Date: Fri, 23 Nov 2007 11:30:53 +0200
>>> >
>>> >Hi All,
>>> >
>>> >I am performing replica exchange molecular dynamics simulation(REMD). I
>>> >have 16 replicas each of which has a peptide with different conformation.
>>> >After obtaining .tpr files (at desired temperatures) for each replicas, I
>>> >loaded them via mdrun, but I got the following error:
>>> >
>>> >Fatal error:
>>> >Nothing to exchange with only one replica
>>> >-------------------------------------------
>>> >
>>> >Why?
>>>
>>>I guess there are two possibilities.
>>>Or you did not use the -np option of mdrun to set the number of replicas,
>>>or you have not compiled Gromacs with MPI support.
>>>
>>>Berk.
>>>
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> 
> -----------------------------------------------------
> XAvier Periole - PhD
> 
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------