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. Program summaryProgram title: BN2DMDCatalogue identifier: AEVJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEVJ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 3120No. of bytes in distributed program, including test data, etc.: 274895Distribution format: tar.gzProgramming 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.
Highlights
Two dimensional models in Molecular Dynamics (MD) simulations have the advantage of quadratic scaling of the number of particles with the system size
In our work we focus on the BN2D water model detailed implementation using Molecular Dynamics
Since MD simulations are performed in the microcanonical ensemble, where entropy S(N, V, E) depends on the number of particles (N), volume (V ), and energy (E), the thermodynamic properties have to be written in terms of time averages of the parameters that can be evaluated during the simulation
Summary
B. Naim, ‘‘Statistical mechanics of ‘waterlike’ particles in two dimensions. I. physical model and application of the Percus–Yevick equation’’, J. A. Dill, ‘‘A simple model of water and the hydrophobic effect’’, J.
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