From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Aug 02 2013 - 15:24:56 CDT
Thanks for answering, Kenno.
Still, there are things in typical NAMD usage that violate momentum conservation (slightly), and that is not great, but probably not horribly wrong, depending on what you purpose is. They are the stochastic forces in the Langevin thermostat, and numerical inaccuracy in the PME force calculation. Anyway, that problem is nowhere near a flying-ice-cube level.
The zeroMomentum option should be helpful.
----- Original Message -----
> Since none of the NAMD developers answered, all I can tell you that
> standard way to calculate temperature in MD software implicitly
> center of mass motion. That said, the standard way to assign initial
> velocities doesn't have any center of mass motion, and in order for
> kind of motion to arise during a simulation, something has to be
> wrong with the integrator or thermostat as to violate conservation of
> momentum. For more information on this subject, Google "Flying Ice
> or look at http://en.wikipedia.org/wiki/Flying_ice_cube
> Using present-day MD software and following best practices will
> prevent this phenomenon from occurring.
> On 08/01/2013 05:53 AM, Norman Geist wrote:
> > Hi experts,
> > just a short and likely simple question:
> > Is the center of mass motion being included in the temperature
> > printed to
> > the log file?
> > Thanks in advance
> > Norman
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