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

[David van der Spoel]

OZGE ENGIN wrote:
> This time, I used the following command line:
> 
> mpirun -np 8 mdrun_mpi -s simul0_md.tpr -replex 2500 -reseed -1 -multi 8
> rename

rename your tpr files to

simul_md0.tpr
simul_md1.tpr
...
simul_md7.tpr

> but 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:
> simul00.tpr
> -------------------------------------------------------
> 
> "Shit Happens" (Pulp Fiction)
> 
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 8
> 
> Although I do not have such a file: simul00.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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se