[gmx-users] problem with mdrun performing replicaexchange MD

[Berk Hess]

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" <OZENGIN at KU.EDU.TR>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>CC: gmx-users at 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" <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.
> >
> >_________________________________________________________________
> >Talk with your online friends with Messenger
> >http://www.join.msn.com/messenger/overview
> >
> >_______________________________________________
> >gmx-users mailing list    gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please search the archive at http://www.gromacs.org/search before 
>posting!
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> >_______________________________________________
> >gmx-users mailing list    gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please search the archive at http://www.gromacs.org/search before 
>posting!
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>_________________________________________________________________
>Play online games with your friends with Messenger
>http://www.join.msn.com/messenger/overview
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Hotmail en Messenger on the move http://www.msn.nl/services