SHAKE - Revision history

Carl McBride: Added an internal link

2011-07-18T15:13:48Z

Added an internal link

← Older revision		Revision as of 17:13, 18 July 2011
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	{{Stub-general}}		{{Stub-general}}
	'''SHAKE''' is an algorithm designed for [[molecular dynamics]] simulation of systems with constraints (e.g. fixed bond-lengths).		'''SHAKE''' is an algorithm designed for [[molecular dynamics]] simulation of systems with constraints (e.g. fixed bond-lengths).
	The constraints are satisfied (almost by construction of the algorithm) at each simulation step.		The constraints are satisfied (almost by construction of the algorithm) at each simulation [[time step]].
	==Variants==		==Variants==
	*[[M-SHAKE]]		*[[M-SHAKE]]

Carl McBride: Added internal links

2011-07-18T14:55:06Z

Added internal links

← Older revision		Revision as of 16:55, 18 July 2011
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	{{Stub-general}}		{{Stub-general}}
	'''SHAKE''' is an algorithm designed for [[molecular dynamics]] simulation of		'''SHAKE''' is an algorithm designed for [[molecular dynamics]] simulation of systems with constraints (e.g. fixed bond-lengths).
	systems with constraints (e.g. fixed bond-lengths).		The constraints are satisfied (almost by construction of the algorithm) at each simulation step.
	The constraints are satisfied (almost by construction of the algorithm) at each simulation		==Variants==
	step.		*[[M-SHAKE]]
			*[[P-SHAKE]]
			*[[Q-SHAKE]]
			*[[RD-SHAKE]]
	==References==		==References==
	#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]		<references/>
	#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]		;Related reading
			*[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
			*[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]
	==External resources==		==External resources==
	*[ftp://ftp.dl.ac.uk/ccp5/ALLEN_TILDESLEY/F.08 Shake algorithm for constraint dynamics of a chain molecule] sample FORTRAN computer code from the book [http://www.oup.com/uk/catalogue/?ci=9780198556459 M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids", Oxford University Press (1989)].		*[ftp://ftp.dl.ac.uk/ccp5/ALLEN_TILDESLEY/F.08 Shake algorithm for constraint dynamics of a chain molecule] sample FORTRAN computer code from the book [http://www.oup.com/uk/catalogue/?ci=9780198556459 M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids", Oxford University Press (1989)].
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Nice and Tidy: Added link to code F.08

2009-02-08T17:26:56Z

Added link to code F.08

← Older revision		Revision as of 19:26, 8 February 2009
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	{{Stub-general}}		{{Stub-general}}
	SHAKE is an algorithm designed for [[molecular dynamics]] simulation of		'''SHAKE''' is an algorithm designed for [[molecular dynamics]] simulation of
	systems with constraints (e.g. fixed bond-lengths).		systems with constraints (e.g. fixed bond-lengths).
	The constraints are satisfied (almost by construction of the algorithm) at each simulation		The constraints are satisfied (almost by construction of the algorithm) at each simulation
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	#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]		#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
	#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]		#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]
			==External resources==
			*[ftp://ftp.dl.ac.uk/ccp5/ALLEN_TILDESLEY/F.08 Shake algorithm for constraint dynamics of a chain molecule] sample FORTRAN computer code from the book [http://www.oup.com/uk/catalogue/?ci=9780198556459 M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids", Oxford University Press (1989)].
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Dduque at 11:26, 12 December 2007

2007-12-12T11:26:03Z

← Older revision		Revision as of 13:26, 12 December 2007
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	{{Stub-general}}		{{Stub-general}}
			SHAKE is an algorithm designed for [[molecular dynamics]] simulation of
			systems with constraints (e.g. fixed bond-lengths).
			The constraints are satisfied (almost by construction of the algorithm) at each simulation
			step.
	==References==		==References==
	#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]		#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
	#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]		#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Nice and Tidy at 10:30, 27 September 2007

2007-09-27T10:30:38Z

← Older revision		Revision as of 12:30, 27 September 2007
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			{{Stub-general}}
	==References==		==References==
	#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]		#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
	#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]		#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Carl McBride: /* References */

2007-07-04T10:17:52Z

References

← Older revision		Revision as of 12:17, 4 July 2007
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	==References==		==References==
	#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]		#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
			#[http://dx.doi.org/10.1080/00268978500101531 Jean-Paul Ryckaert "Special geometrical constraints in the molecular dynamics of chain molecules", Molecular Physics '''55''' pp. 549 - 556 (1985)]
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Carl McBride at 11:43, 12 June 2007

2007-06-12T11:43:28Z

← Older revision		Revision as of 13:43, 12 June 2007
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	==~~REFERENCES~~==		==References==
			#[http://dx.doi.org/10.1016/0021-9991(77)90098-5 Jean-Paul Ryckaert, Giovanni Ciccotti and Herman J. C. Berendsen "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics '''23''' pp.327-341 (1977)]
	[[Category: Molecular dynamics]]		[[Category: Molecular dynamics]]

Carl McBride: New page: ==REFERENCES== Category: Molecular dynamics

2007-06-12T11:37:01Z

New page: ==REFERENCES== Category: Molecular dynamics

New page

==REFERENCES==
[[Category: Molecular dynamics]]