On 12/21/12 12:46 PM, zugunder wrote:
Justin Lemkul wrote
Depends on the algorithm. Pressure is a fickle metric (see
http://www.gromacs.org/Documentation/Terminology/Pressure and previous
discussions on this list). It is generally advisable to run equilibration
using weak coupling (i.e. Berendsen) methods, then switch to a more robust
thermostat and barostat for further equilibration and data collection.
-Justin
Thanks for the explanations, Justin. Talking of thermostats, after some
reading I realized (correct me please if I miss something), that Nose-Hoover
and V-rescale are similar in a sense they introduce corrections into kinetic
energies (though they use different approaches). From this prospective, is
there any preference for any of them for a simple protein-water system?
Probably not in most cases. I can't recall any existing side-by-side comparison
that would make a recommendation for such a "standard" system.
I am asking because in some publications they recommend Nose-Hoover as the
only alternative to simple Berendsen, but when I tried to use it in
Depending on how old the paper is, that may have been true at one time. It is
certainly not true in a general sense that the Nose-Hoover method is the only
alternative to Berendsen. One can, of course, use V-rescale (Bussi thermostat)
or use stochastic dynamics as a means to control temperature.
production MD I got a warning on incompatibility of Nose-Hoover with a
leap-frog integrator, so it switched to a different mode. It doesn't seem to
be a real problem, but since you used V-rescale for both NPT and production
in your tutorial on lysozyme, I think you had certain reason for that.
Not really. During equilibration, one should not use Nose-Hoover until the
system is reasonably stable, so V-rescale represents a good thermostat to use
during that stage, but so is Berensen in that case. For the tutorial, I wanted
to avoid a whole bunch of parameter switching that would lead to a bunch of
questions about why I did it, so I stuck with V-rescale.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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