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On 11/01/2012 11:09 PM, Ester Chiessi wrote:
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<div><font face="Arial" size="2">Thanks Mark.</font></div>
<div><font face="Arial" size="2">Are the results obtained from the
( well behaving ) simulations on A and B platforms reliable ?</font></div>
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<br>
Only after they have equilibrated, and on the evidence of the system
blowing up on C, they didn't start very close to equilibrium.<br>
<br>
Mark<br>
<br>
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<div><font face="Arial" size="2">Ester</font></div>
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<div style="FONT: 10pt arial">----- Original Message ----- </div>
<div style="FONT: 10pt arial; BACKGROUND: #e4e4e4; font-color:
black"><b>From:</b> <a moz-do-not-send="true"
title="Mark.Abraham@anu.edu.au"
href="mailto:Mark.Abraham@anu.edu.au">Mark Abraham</a> </div>
<div style="FONT: 10pt arial"><b>To:</b> <a
moz-do-not-send="true" title="gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">Discussion list for
GROMACS users</a> </div>
<div style="FONT: 10pt arial"><b>Sent:</b> Wednesday, January
11, 2012 12:27 PM</div>
<div style="FONT: 10pt arial"><b>Subject:</b> Re: [gmx-users]
platform dependent fate of a md simulation</div>
<div><br>
</div>
On 11/01/2012 9:18 PM, Ester Chiessi wrote:
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<div><font face="Arial" size="2">Hi,</font></div>
<div> </div>
<div><font face="Arial" size="2">running a md simulation with
the same tpr file ( using Gromacs 4.5.3 ) on three
different platforms ( A: <font face="Times New Roman"
size="3"> </font><font color="#000000" face="Times New
Roman" size="3"><em>HP xw8600 Workstation; B: PC with </em><font
face="Liberation Serif, serif"><font size="3"><font
color="#000000"><em>Intel CORE 2 DUO processor; C:
</em>IBM Power6 cluster ), I obtained the
following results:</font></font></font></font></font></div>
<div> </div>
<div>on A and B platforms the run is fine,</div>
<div>on C the run crashes at the first step, returning LINCS
errors.</div>
<div> </div>
<div><font face="Arial" size="2">Did anyone observe this
behaviour? What does it mean?</font></div>
<div><font face="Arial" size="2">I wonder if my system is
really wrong or not.</font></div>
<div><font face="Arial" size="2">
<div> </div>
<div>I noted this difference in the corresponding md.log
files:</div>
<div>Platform A <span lang="IT">RMS relative
constraint deviation after constraining: 3.56e-06</span></div>
<div>Platform B <span lang="IT">RMS relative
constraint deviation after constraining: 3.48e-06</span></div>
<div>Platform C <span lang="IT">RMS relative
constraint deviation after constraining: 3.58e-06</span></div>
</font></div>
<div> </div>
<div><font face="Arial" size="2">Really many thanks for any
comment.</font></div>
<div><br>
</div>
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<br>
See <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>
for general discussion. Probably A and B are getting lucky with
the numerical integration of a poorly conditioned system, and C
is not. For advice on fixing the problem, see <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
Mark<br>
<p> </p>
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