No, David gave a confusing hint.
If you files are called simul0.tpr simul1.tpr etc.
you should use mdrun -s simul.tpr
mdrun will add the numbers.
With 3.3 you do not need the multi option and -multi does not take an
argument
(but incorrect command line options to mdrun will be ignored).
My original hint was also confusing.
I meant that you should use mpirun with the -np option.
Berk.
From: "OZGE ENGIN" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@gromacs.org
CC: gmx-users@gromacs.org
Subject: Re: Re: RE: [gmx-users] problem with mdrun performing
replicaexchange MD
Date: Fri, 23 Nov 2007 13:10:18 +0200
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" <[EMAIL PROTECTED]>
To: gmx-users@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" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>To: gmx-users@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" <[EMAIL PROTECTED]>
>To: gmx-users@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" <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> >To: gmx-users@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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