Flying ice cube: Difference between revisions

From SklogWiki
Jump to navigation Jump to search
(Added content)
m (Added note)
Line 1: Line 1:
The '''Flying ice cube''' <ref>[http://www3.interscience.wiley.com/journal/33911/abstract Stephen C. Harvey, Robert K.-Z. Tan, Thomas E. Cheatham III "The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition", Journal of Computational Chemistry '''19''' pp. 726-740 (1998)]</ref>
The '''Flying ice cube''' <ref>[http://www3.interscience.wiley.com/journal/33911/abstract Stephen C. Harvey, Robert K.-Z. Tan, Thomas E. Cheatham III "The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition", Journal of Computational Chemistry '''19''' pp. 726-740 (1998)]</ref>
is an artificial situation encountered in [[ molecular dynamics]] simulations. It is due to an incorrect [[equipartition]] of energy
is an artificial situation encountered in [[ molecular dynamics]] simulations. It is due to an incorrect [[equipartition]] of energy
by the [[Thermostats| thermostat]], in particular, by thermostats that implement some form of periodic velocity rescaling, such as the [[Bussi-Donadio-Parrinello thermostat]]. The net result is that an instability forms where the kinetic energy may be drained from some [[Degree of freedom| degrees of freedom]] and be incorrectly fed into others. A manifestation of this would be the kinetic energy from the high frequency bond vibrations and angle bending in a system composed of, say,  flexible [[Water models|water molecules]] ending up in the zero frequency mode of the kinetic energy of the system as a whole (''i.e.'' centre of mass translation); the molecular motions would become frozen, resulting in a ''flying ice cube''.  
by the [[Thermostats| thermostat]], in particular, by thermostats that implement some form of periodic velocity rescaling, such as the [[Bussi-Donadio-Parrinello thermostat]]. The net result is that an instability forms where the kinetic energy may be drained from some [[Degree of freedom| degrees of freedom]] and be incorrectly fed into others. A manifestation of this would be the kinetic energy from the high frequency bond vibrations and angle bending in a system composed of, say,  flexible [[Water models|water molecules]] ending up in the zero frequency mode of the kinetic energy of the system as a whole (''i.e.'' centre of mass translation); the molecular motions would become frozen, resulting in a ''flying ice cube''. Note that despite the name, this situation is not limited to simulations of water.
==Solutions==
==Solutions==
*Use a thermostat that reassigns the velocity distribution, rather than rescaling the actual velocities. (see: [[Andersen thermostat]])
*Use a thermostat that reassigns the velocity distribution, rather than rescaling the actual velocities. (see: [[Andersen thermostat]])

Revision as of 13:34, 20 February 2014

The Flying ice cube [1] is an artificial situation encountered in molecular dynamics simulations. It is due to an incorrect equipartition of energy by the thermostat, in particular, by thermostats that implement some form of periodic velocity rescaling, such as the Bussi-Donadio-Parrinello thermostat. The net result is that an instability forms where the kinetic energy may be drained from some degrees of freedom and be incorrectly fed into others. A manifestation of this would be the kinetic energy from the high frequency bond vibrations and angle bending in a system composed of, say, flexible water molecules ending up in the zero frequency mode of the kinetic energy of the system as a whole (i.e. centre of mass translation); the molecular motions would become frozen, resulting in a flying ice cube. Note that despite the name, this situation is not limited to simulations of water.

Solutions

  • Use a thermostat that reassigns the velocity distribution, rather than rescaling the actual velocities. (see: Andersen thermostat)
  • Reduce the frequency of the velocity rescaling.
  • Increase the temperature bath coupling parameter. (see: Berendsen thermostat)

References

Related reading