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Hi Roland,<br>
<br>
Ah, the -reprod option makes everything consistent between runs now.
The term 'binary reproducibility' in the help message was a bit
confusing at first, but I found the wiki page on reproducibility.<br>
<br>
Thanks for your help,<br>
Matt<br>
<br>
On 01/28/2011 06:29 PM, Roland Schulz wrote:
<blockquote
cite="mid:AANLkTi==eBStcqzaCABhbWQMDeBhjXS2DO=HSJA19swQ@mail.gmail.com"
type="cite">Hi,
<div><br>
</div>
<div>are you running in parallel (either MPI or threads)?
Load-balancing is one reason for different rounding errors.</div>
<div>You can run with "mdrun -reprod" to avoid any different
rounding between runs and should in general get the same then.</div>
<div><br>
</div>
<div>Roland<br>
<br>
<div class="gmail_quote">On Fri, Jan 28, 2011 at 6:17 PM,
Matthew Chan <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mchan3@connect.carleton.ca">mchan3@connect.carleton.ca</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">Hi,<br>
<br>
My second question is about the divergent energy
minimization results which I have been receiving.<br>
<br>
I've taken the 1AKI lysozyme and prepared a single em.tpr
file (1AKI is in vacuum). Afterwards I make 10 copies of the
em.tpr file and use mdrun on each one. If I set the stopping
condition to less than 1000kJ/mol nm, my potential energies
and final structures from each run are not identical. <br>
<br>
I've tried both steepest descent and cg methods for
minimization. I've also checked that the Fmax is indeed less
than my stopping condition, and the potential energy is
negative. Is this problem well documented or is there
something wrong with my system? There seem to be a few parts
of the manual that allude to the possibility of variance
between subsequent runs of EM. <br>
<br>
If this is a well documented problem, can someone try
explaining the cause to me please? I would like to learn
more about this topic.<br>
<br>
Also, the potential energy value reported seems to be
several orders of magnitude different from what other
programs are reporting (24 000 vs 500). What units are it
expressed in?<br>
<br>
Thanks in advance for your replies,<br>
<br>
-- <br>
____________<br>
<font color="#888888"><br>
Matthew Chan<br>
<br>
</font><br>
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