On 25/12/2010 1:12 PM, Qin Qiao wrote:
Thanks a lot!
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?
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..
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 :-)
Mark
Best,
Qin
2010/12/25 David van der Spoel <sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>>
On 12/24/10 6:40 PM, ms wrote:
On 24/12/10 12:26, David van der Spoel wrote:
I'm not an expert, but isn't Berendsen usually not
used because it
doesn't give a correct ensemble? I may be partial
because I personally
know Giovanni Bussi, but it seems from what I've heard
that v-rescale is
the best choice usually.
V-rescale is a good choice. Berendsen not only gives you
the wrong
ensemble but it also biases the energy distribution to
lower energies.
Out of curiosity: why is it still supported in GROMACS?
Wouldn't lead to
less confusion if it is removed? :)
It's still useful for equilibration, e.g. gas to liquid conversion.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
sp...@gromacs.org <mailto:sp...@gromacs.org> http://folding.bmc.uu.se
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