[gmx-users] Re: Question about Berendsen thermostat and

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 24 17:57:52 CEST 2008

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?

(I realize I should know all this, but hey...)

> Best,
> Michael
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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