[gmx-users] Nose-hoover T-coupling in REMD

[Mark Abraham]

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 <spoel at xray.bmc.uu.se 
> <mailto:spoel at 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
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     spoel at gromacs.org <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>     -- 
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