Molecular Dynamics implementation of BN2D or ‘Mercedes Benz‿water model

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• 作者：Arturs Scukins^a ; ^{scukinsa@aston.ac.uk" class="auth_mail" title="E-mail the corresponding author} ; Vitaliy Bardik^b ; ^{vital@univ.kiev.ua" class="auth_mail" title="E-mail the corresponding author} ; Evgen Pavlov^a ; ^b ; ^{e.pavlov@aston.ac.uk" class="auth_mail" title="E-mail the corresponding author} ; Dmitry Nerukh^a ; ^{D.Nerukh@aston.ac.uk" class="auth_mail" title="E-mail the corresponding author}
• 关键词：2D &lsquo ; Mercedes Benz&rsquo ; model ; BN2D ; Molecular Dynamics ; Thermodynamic properties ; Radial distribution function ; Autocorrelation functions ; NVE ; NPT
• 刊名：Computer Physics Communications
• 出版年：2015
• 出版时间：May 2015
• 年：2015
• 卷：190
• 期：Complete
• 页码：129-138
• 全文大小：566 K

文摘

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.

Program summary

Program title: BN2DMD

Catalogue identifier: AEVJ_v1_0

Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEVJ_v1_0.html

Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland

Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html

No. of lines in distributed program, including test data, etc.: 3120

No. of bytes in distributed program, including test data, etc.: 274895

Distribution format: tar.gz

Programming language: C/C++.

Computer: Workstation.

Operating system: Linux, Unix.

Classification: 16.9.

Nature of problem: Molecular dynamics simulation of BN2D or ‘Mercedes Benz’ water model.

Solution method: A BN2D water model [2], microcanonical (NVE) and isothermal–isobaric (NPT) ensembles with velocity-Verlet and Predictor–Corrector integration [1] respectively. Rotational degree of freedom is treated differently in NVE and NPT ensembles due to the nature of the model.

Restrictions: Memory and CPU time limits the size of simulations.

Running time: Depends on the size of system.

References:

[1]

A. B. Naim, “Statistical mechanics of ‘waterlike’ particles in two dimensions. i. physical model and application of the Percus–Yevick equation”, J. Chem. Phys. vol. 54, p. 3682, 1971.

[2]

K. A. T. Silverstein, A. D. J. Haymet, and K. A. Dill, “A simple model of water and the hydrophobic effect”, J. Am. Chem. Soc. vol. 120, pp. 3166–3175, 1998.