Difference between revisions of "MDynaMix"

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(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 ...)
 
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[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.
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[[Image:MeCN-simulation-on-MDynaMix-300.png|300px|thumb|MeCN box simulation on MDynaMix package]]
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[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)]
 
[[Category: Materials modelling and computer simulation codes]]
 
[[Category: Materials modelling and computer simulation codes]]
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== External links ==
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* [http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html Graphical shell for MDynaMix]

Latest revision as of 16:06, 11 February 2010

MeCN box simulation on MDynaMix package

MDynaMix (an acronym for Molecular Dynamics of Mixtures) is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a 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 NVE, NVT and NpT statistical 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 molecular dynamics approach. Package works on Unix/Linux workstations and clusters of workstations as well as on Windows in sequential mode.

References[edit]

  1. 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)

External links[edit]