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<DIV><FONT size=2 face=Arial>Thanks Mark.</FONT></DIV>
<DIV><FONT size=2 face=Arial>Are the results obtained from the ( well
behaving ) simulations on A and B platforms reliable ?</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>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 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 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 size=2 face=Arial>Hi,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>running a md simulation with the same tpr file
( using Gromacs 4.5.3 ) on three different platforms ( A: <FONT size=3
face="Times New Roman"> </FONT><FONT color=#000000 size=3
face="Times New Roman"><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 size=2 face=Arial>Did anyone observe this behaviour? What
does it mean?</FONT></DIV>
<DIV><FONT size=2 face=Arial>I wonder if my system is really wrong or
not.</FONT></DIV>
<DIV><FONT size=2 face=Arial>
<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 size=2 face=Arial>Really many thanks for any
comment.</FONT></DIV>
<DIV><BR> </DIV></BLOCKQUOTE><BR>See <A
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
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</A><BR><BR>Mark<BR>
<P>
<HR>
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