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

[Xavier Periole]

David is write, you need to rename the tpr files is the following cmd:

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
-----------------------------------------------------