From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Aug 02 2013 - 11:15:09 CDT
Since none of the NAMD developers answered, all I can tell you that the
standard way to calculate temperature in MD software implicitly includes
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 this
kind of motion to arise during a simulation, something has to be horribly
wrong with the integrator or thermostat as to violate conservation of
momentum. For more information on this subject, Google "Flying Ice cube"
or look at http://en.wikipedia.org/wiki/Flying_ice_cube
Using present-day MD software and following best practices will completely
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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