From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Apr 22 2004 - 12:02:41 CDT
Hi Alfredo
How is any thermostat not "stochastic" ? At some point you have to decide
to fiddle with an atoms velocity/momentum. Anytime energy/temperature
needs to be adjusted something is wrong or at least modeled incorectly,
no mater how many fancy names you put into a algorithm.
Brian
On Thu, 22 Apr 2004, Juan Alfredo Freites wrote:
> Hi Brian,
>
> I think that we should clarify that STOCHASTIC temperature coupling is
> "bad", in the sense you've indicated, because it precludes energy
> conservation. Let's not forget that one could run a simulation in the
> canonical ensemble by using a Nose-Hoover-chain thermostat, or in the
> isokinetic ensemble using a Gaussian isokinetic thermostat. These I
> would call "good" temperature controls. Of course, these options are not
> available (yet) in NAMD.
>
> Alfredo.
>
> On Thu, 22 Apr 2004, Brian Bennion wrote:
>
> >
> > My training taught me that coupling, especially temperature
> > coupling was "bad", in that you technically start a new simulation
> > everytime you bleed energy off the system.
> >
> > So thats my $0.02
> >
> > Brian
> >
> >
> >
> >
>
> --
> J. Alfredo Freites
> Department of Physics
> University of California, Irvine
> Irvine, CA 92697-4575
> (949) 824-9921
>
>
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**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
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