Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

Arturs Scukins; Vitaliy Bardik; Evgen Pavlov; Dmitry Nerukh

doi:10.1016/j.cpc.2014.12.019

Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

Arturs Scukins^*, Vitaliy Bardik, Evgen Pavlov, Dmitry Nerukh

^*Corresponding author for this work

Abstract

Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

Original language	English
Pages (from-to)	129-138
Number of pages	10
Journal	Computer Physics Communications
Volume	190
Early online date	23 Jan 2015
DOIs	https://doi.org/10.1016/j.cpc.2014.12.019
Publication status	Published - May 2015

Bibliographical note

© 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Funding: RCUK

Keywords

2D 'Mercedes Benz' model
autocorrelation functions
BN2D
molecular dynamics
NPT
NVE
radial distribution function
thermodynamic properties

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10.1016/j.cpc.2014.12.019

Molecular Dynamics implementation of BN2D
© 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) Open Access funded by Engineering and Physical Sciences Research Council under a Creative Commons license CC BY 4.0
Final published version, 566 KBLicence: CC BY 3.0

Cite this

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title = "Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model",

abstract = "Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.",

keywords = "2D 'Mercedes Benz' model, autocorrelation functions, BN2D, molecular dynamics, NPT, NVE, radial distribution function, thermodynamic properties",

author = "Arturs Scukins and Vitaliy Bardik and Evgen Pavlov and Dmitry Nerukh",

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AU - Scukins, Arturs

AU - Bardik, Vitaliy

AU - Pavlov, Evgen

AU - Nerukh, Dmitry

PY - 2015/5

Y1 - 2015/5

N2 - Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

AB - Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

KW - 2D 'Mercedes Benz' model

KW - autocorrelation functions

KW - BN2D

KW - molecular dynamics

KW - NPT

KW - NVE

KW - radial distribution function

KW - thermodynamic properties

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JO - Computer Physics Communications

JF - Computer Physics Communications

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Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

Abstract

Bibliographical note

Keywords

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