[gmx-users] Re: High density after NPT

zugunder schlecht at mail.ru
Fri Dec 21 18:46:25 CET 2012

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? 
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
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.

Thank you.

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