On 16/04/2011 7:06 PM, delara aghaie wrote:
Dear Justin
thanks for your previous explanations.
We are running job with gromacs in parallel. after having the outpus
of the first run, when submitting the jobs for the next 10ns we
encounter with this error. can you help me to fix that. Pleas let me
know the possible reasons to see this kind of error.
Anything could cause that - including some problem with the hardware -
and we can see no diagnostic information. Look at the .log file also.
Try to run the .tpr in serial.
Mark
Thanks
Best wishes
D. Aghaie
*tarting mdrun '3840 water (TIP4P-2005) molecules'
5000000 steps, 10000.0 ps.*
*NOTE: Turning on dynamic load balancing*
*[HPC-0-12.local:26592] *** An error occurred in MPI_Waitall
[HPC-0-12.local:26592] *** on communicator MPI_COMM_WORLD
[HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message truncated
[HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL (your MPI job will now
abort)
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 26592 on
node HPC-0-12 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
*--- On *Sat, 4/16/11, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] the ligand have more than one molecules
To: "Discussion list for GROMACS users" <[email protected]>
Date: Saturday, April 16, 2011, 3:38 AM
ahmet yıldırım wrote:
> Dear users,
>
> Is there anyone has a tutorial of the ligand have more than one
molecules?
Perhaps you can describe in more detail what it is you hope to
accomplish. The procedure for dealing with multiple ligands is,
in principle, no different from a single ligand. There are not
tutorials available for every variation of a procedure.
-Justin
> For example:
> *_topol.top:_*
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> *ligandname * 3
>
> Thanks in advance
> -- Ahmet YILDIRIM
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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