Flying ice cube - Revision history

80.246.140.161: Fixed up page due to recent developments in the literature on the subject

2018-10-20T17:56:01Z

Fixed up page due to recent developments in the literature on the subject

← Older revision		Revision as of 19:56, 20 October 2018
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	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 whereby an incorrect [[equipartition]] of energy is brought about
	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.		by [[Thermostats\| thermostats]] that improperly implement some form of periodic velocity rescaling outside of the continuous equations of motion, such as the [[Berendsen thermostat]].
	~~==Solutions==~~		The artifact is due to these thermostats violating the balance condition that is a requirement of Monte Carlo simulations ([[ molecular dynamics ]] simulations with velocity rescaling thermostats can be thought of as Monte Carlo simulations with [[ molecular dynamics]] moves and velocity rescaling moves).<ref name="Braun et al">[http://doi.org/10.1021/acs.jctc.8b00446 Efrem Braun, Seyed M. Moosavi, Berend Smit "Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited", Journal of Chemical Theory and Computation '''14''' pp. 5262-5272 (2018)]</ref>
	*Use a thermostat that ~~reassigns~~ the ~~velocity distribution~~, ~~rather than rescaling~~ the ~~actual velocities. (see:~~ [[~~Andersen~~ 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.
	*Reduce the frequency of the velocity rescaling.		This artifact is avoided by using a velocity rescaling thermostat that obeys the balance condition, such as the [[Bussi-Donadio-Parrinello thermostat]].<ref name="Braun et al"/>
	*Increase the temperature bath coupling parameter. (see: [[Berendsen thermostat]])
	==References==		==References==
	<references/>		<references/>
	;~~Related reading~~		;
	*[http://dx.doi.org/10.1007/s40436-013-0024-3 Liu-Ming Yan, Chao Sun, Hui-Ting Liu "Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water", Advances in Manufacturing '''1''' pp. 160-165 (2013)]
	[[category: molecular dynamics]]		[[category: molecular dynamics]]

Carl McBride: Added note

2014-02-20T12:34:02Z

Added note

← Older revision		Revision as of 14:34, 20 February 2014
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	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]])

Carl McBride: Added content

2014-02-20T12:31:14Z

Added content

← Older revision		Revision as of 14:31, 20 February 2014
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	~~{{stub-general}}~~		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>
	'''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
			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''.
			==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==		==References==
	<references/>		<references/>
			;Related reading
	*[http://dx.doi.org/10.1007/s40436-013-0024-3 Liu-Ming Yan, Chao Sun, Hui-Ting Liu "Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water", Advances in Manufacturing '''1''' pp. 160-165 (2013)]		*[http://dx.doi.org/10.1007/s40436-013-0024-3 Liu-Ming Yan, Chao Sun, Hui-Ting Liu "Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water", Advances in Manufacturing '''1''' pp. 160-165 (2013)]
	[[category: molecular dynamics]]		[[category: molecular dynamics]]

Carl McBride: Added a related publication

2014-02-19T14:50:06Z

Added a related publication

← Older revision		Revision as of 16:50, 19 February 2014
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	==References==		==References==
	<references/>		<references/>
			*[http://dx.doi.org/10.1007/s40436-013-0024-3 Liu-Ming Yan, Chao Sun, Hui-Ting Liu "Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water", Advances in Manufacturing '''1''' pp. 160-165 (2013)]
	[[category: molecular dynamics]]		[[category: molecular dynamics]]

Carl McBride: New page: {{stub-general}} '''Flying ice cube''' [http://www3.interscience.wiley.com/journal/33911/abstract Stephen C. Harvey, Robert K.-Z. Tan, Thomas E. Cheatham III "The flying ice cube: Vel...

2010-07-20T11:57:42Z

New page: {{stub-general}} '''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: Vel...

New page

{{stub-general}}
'''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>
==References==
<references/>
[[category: molecular dynamics]]