[gmx-users] Re: Question about Berendsen thermostat and
Hans Martin Senn
senn at chem.gla.ac.uk
Thu Jul 24 18:09:12 CEST 2008
On 24 Jul 2008, at 16:57, David van der Spoel wrote:
> Michael Shirts wrote:
>>>> Thanks for the tip!
>> You're welcome!
>>>> That thermostat is really nice and also simple to implement.
>>>> It is now in CVS.
>>> If this thermostat has a stochastic term, is the dynamics still
>>> meaningful then?
>> Of course it's not! No thermostat gives physical dynamics. But at
>> least it gives the canonical distribution at equilibrium!
> Well in that case I'm not sure what is more important for me. It
> depends on the application I presume.
> But does the NH chain, the mother of all thermostats, indeed yield
> correct dynamics?
Yes, it does. Always assuming that you couple only one (NH) thermostat
to the system. The other thermostats in the NH chain then are
successively coupled to one another, not to the physical system. For
the proof that NH does indeed create a canonical ensemble (see the
original NH papers), these "thermostats of thermostats" don't really
> (I realize I should know all this, but hey...)
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow
E-mail: senn at chem.gla.ac.uk
Direct line: +44 (0)141 330 6574
Fax: +44 (0)141 330 4888
Department of Chemistry
Joseph Black Building
University of Glasgow
Glasgow G12 8QQ
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