Hi John,
thanks a lot for your comments. I will have a closer look on the paper
that you mentioned.
Cheers,
Jochen
John D. Chodera wrote:
Hi Jochen,
I think the paper you are referring to is this one, commonly cited on
the AMBER mailing list and by others in support of the idea that there
is little difference between Berendsen and Nose-Hoover:
* T. Morishita. Fluctuation formulas in molecular-dynamics simulations
with the weak coupling heat bath. J. Chem. Phys., 113(8):2976, 2000.
However, this paper actually concludes the opposite:
"The present study shows that the WC thermostat does not produce the
canonical ensemble but another ensemble."
The paper demonstrates that, in the limit as the coupling time \tau ->
0, the isokinetic ensemble is produced, while in the limit that \tau
-> \infinity, the microcanonical ensemble is produced.
For expectations involving only coordinates (and not momenta), the
agreement with the canonical ensemble is achieved only if terms on the
order of 1/N are neglected -- which is precisely the rate at which all
ensembles become equivalent, the "thermodynamic limit". In other
words, if your system is big enough to reach the "thermodynamic limit"
(and who knows how big that is?) then you are just as well off using
*any* ensemble -- NVE, NPT, NPH, NVT -- it doesn't matter anymore.
Allen and Tildesley, for example, states on the difference between
ensembles: "the small relative magnitude of the correction term can be
seen explicitly: it decreases as O(N^-1)." (pg. 45 in my edition)
So only in the thermodynamic limit will there be correspondence
between Berendsen and Nose-Hoover ensembles for properties dependent
on the configuration space distribution. Whether your system is large
enough to have reached this limit is something that you will have to
establish for yourself.
However, if you are interested in kinetic properties and make use of
the Berendsen weak-coupling algorithm, you will likely want to
investigate whether there is any \tau dependence in your computed
properties or observed behavior, since the width of the kinetic energy
distribution is a strong function of \tau.
Cheers,
- John
--
Dr. John D. Chodera <[EMAIL PROTECTED]> | Mobile : 415.867.7384
Postdoctoral researcher, Pande lab | Lab phone : 650.723.1097
Department of Chemistry, Stanford University | Lab fax : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera
Date: Mon, 15 Oct 2007 15:37:40 +0200
From: Jochen Hub <[EMAIL PROTECTED]>
Subject:
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi,
I think there is a paper around which says that for parcticle purposes
it hardly matters whether one uses Berendsen or Nose-Hoover T-coupling.
Does anyone remember the reference?
Thanks in advance,
Jochen
--************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
.
--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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