Hi all,
One of the conceptual difference between Berendsen and Nose-Hoover (NH),
is the following. NH is basically a second order relaxation to the
target temperature, which implies an oscillatory behavior. Berendsen is
a first order relaxation (exponential type of behavior). This is
preferable when the initial temperature is far from the target
temperature, in which case NH is likely to produce large oscillations
and, in general, take longer to equilibrate. Hence the practice to use
Berendsen for the first part of the equilibration, and NH for production.
There are still papers published on the subject in the "alive"
literature. For example there is an analysis of the Berendsen dynamics in
Morishita, JCP 113 (8) : 2976 (2000)
In short, he finds approximate expressions for the configurational part
of the state distribution function. It essentially varies between
canonical for exceedingly small time constants (of the order of the
timestep) to microcanonical for very large time constants. The
distribution of momenta remains unknown.
In addition to the average temperature, the temperature fluctuations
expected for the NVT ensemble must be reproduced in the simulation.
Nose-Hoover was shown to do this correctly. This could be important when
studying the stability of a conformation for example.
Now concerning Chris' question:
[EMAIL PROTECTED] wrote:
Have you seen any information to suggest that this is actually a
non-trivial conce"rn? That is, given static point charges, an
empirical LJ force, short cutoffs, etc., do you believe that the
application of nose-hoover, berendsen, or even the arbitrary velocity
rescaling significantly degrades the quality of the obtained dynamics?
There are two aspects here: (a) point charges and LJ force, which
constitute the physical model, and (b) the cutoffs and such, which are
simulation artefacts and disrupt the physics of the model (by allowing
creation of energy, etc...). My opinion is that, given a physical model
(even approximate), one should simulate the dynamics as accurately as
possible, in order to produce the thermodynamical ensemble corresponding
to the underlying physical model. Before plugging in the thermostat, one
should check that the simulation conserves energy "not too bad"(using
PME or switch functions, etc...). Now if there is still an energy drift,
the thermostat will absorb the excess energy, and the system will end up
in a non-equilibrium steady state, with a heat well (cutoffs, etc) and a
heat sink (thermostat). The good side is that the NH thermostat was
shown (by Hoover himself) to produce a stationary canonical distribution
even in a non-equilibrium case.
Sorry for the long email :)
Michel
--
==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
http://ludwig-sun1.unil.ch/~mcuendet
==========================================================
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