[gmx-developers] Various integrator questions . . .

David spoel at xray.bmc.uu.se
Tue Aug 9 18:49:28 CEST 2005

> > Second, the Nose-Hoover thermostat gives the correct ensemble for your
> > system plus "something else". In fact it therefore does not give you the
> > correct ensemble for what you are interested in.
> I think Michel addressed this before -- for the physical variables,
> you get the correct canonical
> distribution.
But not necessarily the correct fluctuations, as described in the
GROMACS manual (probably written by Berk, but I'm not sure). This means
that averages may be correct, and possibly also the amplitude of the
fluctuations, but the time structure of the fluctuations is artificial.
Higher moments may also be affected.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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