ms2: A molecular simulation tool for thermodynamic properties, release 3.0-猫眼课题宝

DOI：

10.1016/j.cpc.2017.07.025

发表时间：

2017-12

期刊：

Comput. Phys. Commun.

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

Gábor Rutkai;Andreas Köster;G. Guevara-Carrión;T. Janzen;Michael Schappals;Colin W. Glass;M. Bernreuther;Amer Wafai;S. Stephan;M. Kohns;Steffen Reiser;Stephan Deublein;M. Horsch;Hans Hasse;J. Vrabec

摘要介绍了分子模拟工具ms2的新版本（3.0）（Deublein et al., 2011; Glass et al. 2014）。ms 2的3.0版本增加了两个额外的系综，即微正则系综（N V E）和等压-等焓系综（N p H）， N V E系综中的各种亥姆霍兹能量导数，用于计算化学势的热力学积分，用于计算溶剂活度的渗透压，四元混合物的六个麦克斯韦-斯蒂芬扩散系数，采样氢键的统计数据，平滑粒子网格埃瓦尔德求和以及在单个程序执行中执行任意数量的状态点的分子动力学运行的能力。新版本程序摘要程序标题：m s 2程序文件doi: http://dx。doi。org/10.17632/9rcrykvkyh。1许可条款：CC by NC 3.0编程语言：Fortran95补充资料：补充资料中详细描述了热力学集成和氢键的参数设置。此外，我们小组开发的所有分子力场模型都提供了以前版本的期刊参考：Deublein et al., Comput.。理论物理。common . 182 (2011) 2350 and Glass et al., Comput。理论物理。common . 185(2014) 3302新版本是否取代旧版本？：是新版本原因：引入新功能，提高计算效率两个新的系综（N V E和N p H），新的性质（亥姆霍兹能量导数，通过热力学积分的化学势，通过渗透压的活度系数，第四系混合物的麦克斯韦-斯蒂芬扩散系数），新的功能（氢键的检测和统计，光滑粒子网格埃瓦尔德求和，在单个程序执行中对任意数量的状态点进行分子动力学运行的能力）。问题性质：计算面向应用的热力学性质：纯流体和多组分混合物的气液平衡，热，热量和熵数据以及输运性质和微观结构数据。解决方法：分子动力学，蒙特卡罗，各种系综，大平衡法，Green-Kubo形式，Lustig形式，OPAS方法，光滑粒子网格Ewald求和。ms2解决的典型问题是通过模拟包含1000到5000个分子的系统来解决的，这些分子被建模为刚体。其他注释：文档可从http://www获得。ms-2。德

Abstract A new version release (3.0) of the molecular simulation tool ms 2 (Deublein et al., 2011; Glass et al. 2014) is presented. Version 3.0 of ms 2 features two additional ensembles, ie microcanonical (N V E) and isobaric–isoenthalpic (N p H), various Helmholtz energy derivatives in the N V E ensemble, thermodynamic integration as a method for calculating the chemical potential, the osmotic pressure for calculating the activity of solvents, the six Maxwell–Stefan diffusion coefficients of quaternary mixtures, statistics for sampling hydrogen bonds, smooth-particle mesh Ewald summation as well as the ability to carry out molecular dynamics runs for an arbitrary number of state points in a single program execution. New version program summary Program Title: m s 2 Program Files doi: http://dx. doi. org/10.17632/9rcrykvkyh. 1 Licensing provisions: CC by NC 3.0 Programming language: Fortran95 Supplementary material: A detailed description of the parameter setup for thermodynamic integration and hydrogen bonding is given in the supplementary material. Furthermore, all molecular force field models developed by our group are provided Journal reference of previous versions: Deublein et al., Comput. Phys. Commun. 182 (2011) 2350 and Glass et al., Comput. Phys. Commun. 185 (2014) 3302 Does the new version supersede the previous version?: Yes Reasons for the new version: Introduction of new features as well as enhancement of computational efficiency Summary of revisions: Two new ensembles (N V E and N p H), new properties (Helmholtz energy derivatives, chemical potential via thermodynamic integration, activity coefficients via osmotic pressure, Maxwell–Stefan diffusion coefficients of quaternary mixtures), new functionalities (detection and statistics of hydrogen bonding, smooth-particle mesh Ewald summation, ability to carry out molecular dynamics runs for an arbitrary number of state points in a single program execution). Nature of problem: Calculation of application oriented thermodynamic properties: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal, caloric and entropic data as well as transport properties and data on microscopic structure Solution method: Molecular dynamics, Monte Carlo, various ensembles, Grand Equilibrium method, Green–Kubo formalism, Lustig formalism, OPAS method, smooth-particle mesh Ewald summation Restrictions: Typical problems addressed by m s 2 are solved by simulating systems containing 1000 to 5000 molecules that are modeled as rigid bodies. Additional comments: Documentation is available at http://www. ms-2. de

ms2: A molecular simulation tool for thermodynamic properties, release 3.0

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