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>
<br>Best,<br><br>Qin <br><br><div class="gmail_quote">2010/12/25 David van der Spoel <span dir="ltr"><<a 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>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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