[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling

[chris.neale at utoronto.ca]

Thanks David for sharing your knowledge, especially the note that for  
further information one can refer to the literature that was written  
around the time that these thermostats were released. I have a  
question though:

> by the way it is also true that if you use a thermostat or barostat  
> then although long time averages are equivalent to averages in the  
> NVT or NPT ensemble strictly the dynamics is no longer valid as
> a Newtonian trajectory so you should not derive dynamic properties  
> from such trajectories.

Have you seen any information to suggest that this is actually a  
non-trivial concern? 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?

Thanks,
Chris.