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On 16/04/2011 7:06 PM, delara aghaie wrote:
<blockquote cite="mid:443865.45462.qm@web130124.mail.mud.yahoo.com"
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<div>Dear Justin</div>
<div>thanks for your previous explanations.</div>
<div>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.</div>
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<br>
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.<br>
<br>
Mark<br>
<br>
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<div>Thanks</div>
<div>Best wishes</div>
<div>D. Aghaie</div>
<div><br>
<strong><font color="#0000bf">tarting mdrun '3840 water
(TIP4P-2005) molecules'<br>
5000000 steps, 10000.0 ps.</font></strong></div>
<div><strong><font color="#0000bf">NOTE: Turning on
dynamic load balancing</font></strong></div>
<div><strong><font color="#0000bf">[HPC-0-12.local:26592]
*** An error occurred in MPI_Waitall<br>
[HPC-0-12.local:26592] *** on communicator
MPI_COMM_WORLD<br>
[HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message
truncated<br>
[HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL
(your MPI job will now abort)<br>
--------------------------------------------------------------------------<br>
mpirun has exited due to process rank 2 with PID
26592 on<br>
node HPC-0-12 exiting without calling "finalize".
This may<br>
have caused other processes in the application to be<br>
terminated by signals sent by mpirun (as reported
here).<br>
</font></strong>--- On <b>Sat, 4/16/11, Justin A.
Lemkul <i><a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></i></b> wrote:<br>
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From: Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
Subject: Re: [gmx-users] the ligand have more than one
molecules<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Saturday, April 16, 2011, 3:38 AM<br>
<br>
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<br>
ahmet yıldırım wrote:<br>
> Dear users,<br>
> <br>
> Is there anyone has a tutorial of the ligand have
more than one molecules?<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
> For example:<br>
> *_topol.top:_*<br>
> [ molecules ]<br>
> ; Compound #mols<br>
> Protein_chain_A 1<br>
> Protein_chain_B 1<br>
> *ligandname * 3<br>
> <br>
> Thanks in advance<br>
> -- Ahmet YILDIRIM<br>
> <br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
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<br>
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