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On 1/04/2011 6:52 PM, bsmith wrote:
<blockquote
cite="mid:D03A28BF-C526-4A69-8CC0-FA0931B47AF1@wehi.edu.au"
type="cite">
<div>On 01/04/2011, at 6:29 PM, Mark Abraham wrote:</div>
<div>
<div><br class="Apple-interchange-newline">
<blockquote type="cite">
<div>On 1/04/2011 6:03 PM, Ruchi Gupta wrote:<br>
<blockquote type="cite">Dear gmx-users,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I am facing some problems while
running replica exchange MD using Gromacs.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Few seconds after the job
submission it ends with the following error message:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">"<br>
</blockquote>
<blockquote type="cite">Initializing Replica Exchange<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Repl There are 6 replicas:<br>
</blockquote>
<blockquote type="cite">Multi-checking the number of atoms
... OK<br>
</blockquote>
<blockquote type="cite">Multi-checking the integrator ...
OK<br>
</blockquote>
<blockquote type="cite">Multi-checking init_step+nsteps
...<br>
</blockquote>
<blockquote type="cite">init_step+nsteps is not equal for
all subsystems<br>
</blockquote>
<blockquote type="cite"> subsystem 0: 0<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"> subsystem 1: 50000<br>
</blockquote>
<blockquote type="cite"> subsystem 2: 0<br>
</blockquote>
<blockquote type="cite"> subsystem 3: 50000<br>
</blockquote>
<blockquote type="cite"> subsystem 4: 0<br>
</blockquote>
<blockquote type="cite"> subsystem 5: 50000<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-------------------------------------------------------<br>
</blockquote>
<blockquote type="cite">Program mdrun, VERSION 4.5.4<br>
</blockquote>
<blockquote type="cite">Source code file: main.c, line:
249<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Fatal error:<br>
</blockquote>
<blockquote type="cite">The 6 subsystems are not
compatible<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">For more information and tips for
troubleshooting, please check the GROMACS<br>
</blockquote>
<blockquote type="cite">website at<a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-------------------------------------------------------<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">"<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I am using a "single .gro file"
and "6 different md.mdp" files (at 6 different
temperatures) for generating "6 .tpr files",
respectively. But the simulation doesn't work.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">I have compared the ".tpr files"
using "gmxdump" and "gmxcheck" Gromacs commands and they
seem fine with respect to nsteps and init_step
information.<br>
</blockquote>
<br>
So, to be clear, gmxcheck says that for no pair of .tprs
does init_step or nsteps differ...<br>
<br>
What is your mdrun command line? Are you using checkpoint
files?<br>
<br>
Mark<br>
-- <br>
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</div>
</blockquote>
</div>
<br>
</div>
1) Comparison of the .tpr files using gmxdump reveals no
differences but for the temperatures and the velocities in each
i.e. init_step and nsteps have the same values (0 and 50000,
respectively) in all files.
<div><br>
</div>
<div>2) We have tried running mdrun without checkpointing (-cpt
-1) and with checkpointing with no change in the outcome.</div>
</blockquote>
<br>
That sounds like a bug. Please create a new Redmine issue here
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org">http://redmine.gromacs.org</a> and attach your .tpr and .mdp files -
preferably in a compressed archive file. You should get the option
to assign it to me - please do.<br>
<br>
Mark<br>
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