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On 1/04/2012 5:51 PM, Acoot Brett wrote:
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cite="mid:1333266679.69140.YahooMailNeo@web121804.mail.ne1.yahoo.com"
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<div><span>Hi Mark,</span></div>
<div><span></span> </div>
<div><span>Then can you explain in which situation the
calculation could be error and how to avoid it?</span></div>
</div>
</blockquote>
<br>
One could write a book in partial answer to this question. There are
lots of things we don't yet know because we can't afford to run
calculations that might yield knowledge. Ultimately, a model of
physics is about as good as its capacity to reproduce findings from
real physics, and so the goal of simulators should be to use methods
that have been shown to do that well. Showing good performance can
be tricky, as converged equilibrium distributions are normally very
expensive to obtain. Also, different observables might require
different methods for good agreement with experiment, so there is no
general answer for how to do things right, unfortunately.<br>
<br>
Mark<br>
<br>
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cite="mid:1333266679.69140.YahooMailNeo@web121804.mail.ne1.yahoo.com"
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<div><span></span> </div>
<div><span>Cheers,</span></div>
<div><span></span> </div>
<div><span>Acoot</span></div>
<div><br>
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<div dir="ltr"> <font face="Arial" size="2"> <b><span
style="font-weight: bold;">From:</span></b> Mark
Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Sunday, 1 April 2012 5:47 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] Possible error in the gromacs
calculation<br>
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<div> On 1/04/2012 5:44 PM, Acoot Brett wrote:
<blockquote type="cite">
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new roman, new york, times, serif; font-size: 12pt;
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<div><span>Dear All,</span></div>
<div><span></span> </div>
<div><span>For the GROMACS 4.5.5, after installation
the test link is unavaliable, thus we cannot run
the test.</span></div>
<div><span></span> </div>
<div><span>For the AMBER, after we install it and
run the test, although we can pass most of the
tests, we cannot pass all of the tests.</span></div>
<div><span></span> </div>
<div><span>For GROMACS, can there anything wrong for
the calculation, just as if we cannot pass all
the test for AMBER?</span></div>
<div><span></span> </div>
<div><span>For the caluclation itself, in which
situation we can get the wrong calculation
results? And how should we solve the problems if
we the calculation can give wrong results by
default?</span></div>
</div>
</blockquote>
<br>
Unfortunately there is not an effective test set for
GROMACS at the moment. There is work taking place to get
one, but it will not be ready before 4.6.<br>
<br>
Mark<br>
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