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On 25/12/2010 1:12 PM, Qin Qiao wrote:
<blockquote
cite="mid:AANLkTikN++gXLBHq2p2Q9-MvJcKAfJ3pXG4RqKJhoyNr@mail.gmail.com"
type="cite">Thanks a lot! <br>
<br>
It says Nose-hoover coupling generates the correct canonical
ensemble, and that's the reason why I used it. I wonder whether
v-rescale can also get the correct ensemble. Could you tell me?<br>
<br>
I'm quite curious how to choose the frequency of the T-coupling in
REMD. Though it seems the higher the frequency, the more accurate
T will be, I wonder whether it will get artifacts for in MD run..
since the warning in Gromacs says tau_t should be 20 times bigger
than dt*nsttcouple..<br>
</blockquote>
<br>
Consider what you mean by "accurate T". You actually wish to sample
from a given "constant" temperature ensemble. However that ensemble
does not show its average T at every instant - the conserved
quantity is not actually temperature. What you want is the right
average T and the right fluctuations. Probably you want to read the
literature for the T-coupling algorithms to learn more about the
details here... Probably I should also too :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTikN++gXLBHq2p2Q9-MvJcKAfJ3pXG4RqKJhoyNr@mail.gmail.com"
type="cite">
<br>
Best,<br>
<br>
Qin <br>
<br>
<div class="gmail_quote">2010/12/25 David van der Spoel <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">On 12/24/10 6:40 PM, ms wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
On 24/12/10 12:26, David van der Spoel wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
I'm not an expert, but isn't Berendsen usually not
used because it<br>
doesn't give a correct ensemble? I may be partial
because I personally<br>
know Giovanni Bussi, but it seems from what I've heard
that v-rescale is<br>
the best choice usually.<br>
<br>
</blockquote>
V-rescale is a good choice. Berendsen not only gives you
the wrong<br>
ensemble but it also biases the energy distribution to
lower energies.<br>
</blockquote>
<br>
Out of curiosity: why is it still supported in GROMACS?
Wouldn't lead to<br>
less confusion if it is removed? :)<br>
<br>
</blockquote>
</div>
It's still useful for equilibration, e.g. gas to liquid
conversion.<br>
<br>
-- <br>
David.<br>
________________________________________________________________________<br>
<font color="#888888">
David van der Spoel, PhD, Professor of Biology<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: 46 18 471 4205 fax: 46 18 511 755<br>
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target="_blank">spoel@xray.bmc.uu.se</a> <a
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