Code for molecular dynamics simulation of two dimensional Mercedes-Benz water model

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Computer Physics Communications Pub Date : 2024-06-06 DOI:10.1016/j.cpc.2024.109267

Peter Ogrin , Cristiano L. Dias , Tomaz Urbic

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Abstract

The Mercedes-Benz (MB) water model is a simple two-dimensional toy model of water that can reproduce many of the anomalous properties of water. Within the model, the water particles are represented as Lennard-Jones disks with explicitly added orientation-dependent interactions that mimic the formation of hydrogen bonds. Due to the simple implementation of the MB model in Monte Carlo simulations, it was mainly studied with Monte Carlo simulations in different ensembles. The implementation of the model in molecular dynamics simulations is not trivial. In this paper we present the code for molecular dynamics simulations. The structural and thermodynamic properties of the model were calculated using molecular dynamics and compared with data from Monte Carlo simulations to confirm that the molecular dynamics code works correctly. We also used molecular dynamics to calculate the dynamic properties of the model. The Fortran source code of our molecular dynamics simulation of the MB water model is provided.

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二维梅赛德斯-奔驰水模型分子动力学模拟代码

梅赛德斯-奔驰（MB）水模型是一个简单的二维水玩具模型，可以再现水的许多异常特性。在该模型中，水粒子被表示为 Lennard-Jones 盘，并明确添加了取向相关的相互作用，以模拟氢键的形成。由于 MB 模型在蒙特卡罗模拟中的实现比较简单，因此主要通过不同集合的蒙特卡罗模拟进行研究。在分子动力学模拟中实现该模型并非易事。本文介绍了分子动力学模拟的代码。我们利用分子动力学计算了该模型的结构和热力学性质，并与蒙特卡罗模拟的数据进行了比较，以确认分子动力学代码工作正常。我们还利用分子动力学计算了模型的动态特性。我们提供了 MB 水模型分子动力学模拟的 Fortran 源代码。

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来源期刊

Computer Physics Communications 物理-计算机：跨学科应用

CiteScore

12.10

自引率

3.20%

发文量

287

审稿时长

5.3 months

期刊介绍： The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper. Computer Programs in Physics (CPiP) These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged. Computational Physics Papers (CP) These are research papers in, but are not limited to, the following themes across computational physics and related disciplines. mathematical and numerical methods and algorithms; computational models including those associated with the design, control and analysis of experiments; and algebraic computation. Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.