MDynaMix - Revision history

Nice and Tidy at 14:06, 11 February 2010

2010-02-11T14:06:23Z

← Older revision		Revision as of 16:06, 11 February 2010
Line 1:		Line 1:
	[[Image:MeCN-simulation-on-MDynaMix-300.png\|300px\|thumb\|MeCN box simulation on MDynaMix package]]		[[Image:MeCN-simulation-on-MDynaMix-300.png\|300px\|thumb\|MeCN box simulation on MDynaMix package]]

	[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[~~Boundary~~ conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the double [[time step]] algorithm is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.		[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Periodic boundary conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the double [[time step]] algorithm is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.
	==References==		==References==
	#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]		#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]

Carl McBride: Changed internal link to time step.

2010-01-21T13:30:23Z

Changed internal link to time step.

← Older revision		Revision as of 15:30, 21 January 2010
Line 1:		Line 1:
	[[Image:MeCN-simulation-on-MDynaMix-300.png\|300px\|thumb\|MeCN box simulation on MDynaMix package]]		[[Image:MeCN-simulation-on-MDynaMix-300.png\|300px\|thumb\|MeCN box simulation on MDynaMix package]]

	[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the [[~~double~~ time step ~~algorithm~~]] is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.		[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the double [[time step]] algorithm is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.
	==References==		==References==
	#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]		#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]

193.232.68.75: /* External links */

2010-01-21T13:04:07Z

External links

← Older revision		Revision as of 15:04, 21 January 2010
Line 7:		Line 7:

	== External links ==		== External links ==
	* [http://www.~~agilemolecule~~.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]		* [http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]

Niki at 22:26, 17 April 2009

2009-04-17T22:26:44Z

← Older revision		Revision as of 00:26, 18 April 2009
Line 1:		Line 1:
	[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the [[double time step algorithm]] is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach.		[[Image:MeCN-simulation-on-MDynaMix-300.png\|300px\|thumb\|MeCN box simulation on MDynaMix package]]

			[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] (an acronym for '''M'''olecular '''Dyna'''mics of '''Mix'''tures) is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields \|force field]] consisting of [[Lennard-Jones model \|Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions \|periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the [[double time step algorithm]] is used. Algorithms for [[Microcanonical ensemble \|NVE]], [[Canonical ensemble \|NVT]] and [[Isothermal-isobaric ensemble \|NpT]] statistical [[Ensembles in thermostatistics \|ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation \|path integral molecular dynamics]] approach. Package works on ''Unix/Linux'' workstations and clusters of workstations as well as on ''Windows'' in sequential mode.
	==References==		==References==
	#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]		#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]
	[[Category: Materials modelling and computer simulation codes]]		[[Category: Materials modelling and computer simulation codes]]

			== External links ==
			* [http://www.agilemolecule.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]

Carl McBride: New page: [http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by ...

2009-03-04T12:45:07Z

New page: [http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by ...

New page

[http://www.fos.su.se/~sasha/mdynamix/ MDynaMix] is a general purpose [[molecular dynamics]] code for simulations of [[mixtures]] of either rigid or [[flexible molecules]], interacting by a [[Force fields |force field]] consisting of [[Lennard-Jones model |Lennard-Jones]], electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a [[Boundary conditions |periodic rectangular, hexagonal or truncated octahedron cell]]. Rigid bonds are constrained by the [[SHAKE]] algorithm. In case of flexible molecular models the [[double time step algorithm]] is used. Algorithms for [[Microcanonical ensemble |NVE]], [[Canonical ensemble |NVT]] and [[Isothermal-isobaric ensemble |NpT]] statistical [[Ensembles in thermostatistics |ensembles]] are implemented, as well as [[Ewald sum]] for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the [[Path integral formulation |path integral molecular dynamics]] approach.
==References==
#[http://dx.doi.org/10.1016/S0010-4655(99)00529-9 Alexander P. Lyubartsev and Aatto Laaksonen "M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures", Computer Physics Communications '''128''' pp. 565-589 (2000)]
[[Category: Materials modelling and computer simulation codes]]