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If you are only interested in conformational sampling, then it makes
sense to start at 300 K or even higher - maybe 320 K. The main
reason for working at lower temperatures is if your system <br>
is unstable - eg. if you expect that the molecule will be mostly
unfolded at 300 K and you want to sample the folded state. Another
reason might be having experimental data at lower T, but this<br>
is problematic, as it is hard to model temperature-dependent
properties with simple force fields.<br>
<br>
Krzysztof Kuczera<br>
<br>
On 4/27/12 10:06 AM, Tomek Wlodarski wrote:
<blockquote
cite="mid:CANAOJCuHJeNYjNJb_Sntvxw1cuSydEx=zgf=pGC9e5VXGM5hHQ@mail.gmail.com"
type="cite">
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Hi Mark,
<div><br>
</div>
<div>Thanks for reply.</div>
<div><br>
</div>
<div>The problem is that I have never found in the papers
reasoning behind the the lower than 300K temperatures.</div>
<div>Moreover, authors were interested in properties in 300K or
above.</div>
<div>I was wondering if this is not based on experience that REMD
implemented in gromacs works better when you also include lower
temperature.?</div>
<div>best!</div>
<div><br>
</div>
<div>tomek<br>
<div><br>
<div>
On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham <span><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote>
<div>
<div>On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:<br>
<blockquote>
Hi,<br>
<br>
I have notice that quite often people in REMD
simulation use replicas in lower than 300K temp.<br>
Using for example temperature ranges from 250 to
450K<br>
I am wondering what is the purpose of those
replicas.<br>
I have limited computational resources and I am
wondering if for studing 175 aa protein is better to
start from 250K and up to 350 K or choose from
300-400K (just an example)<br>
<br>
</blockquote>
<br>
</div>
</div>
Depends on the temperature(s) at which you wish to make
observations. Sampling is normally enhanced at higher
temperatures, so unless you want the ensemble at some low
temperatures, it is normal to start at your lowest
observation temperature.<br>
<br>
Of course, you could always read the reasoning provided by
the authors in their paper, or email them for
clarification...<span> <br>
<br>
Mark<br>
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<br>
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<pre class="moz-signature" cols="72">--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: <a class="moz-txt-link-abbreviated" href="mailto:kkuczera@ku.edu">kkuczera@ku.edu</a>
<a class="moz-txt-link-freetext" href="http://oolung.chem.ku.edu/~kuczera/home.html">http://oolung.chem.ku.edu/~kuczera/home.html</a>
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