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

A new version release (3.0) of the molecular simulation tool ms2 (Deublein et al., 2011; Glass et al.. 2014) is presented. Version 3.0 of ms2 features two additional ensembles, i.e. microcanonical (NVE) and isobaric–isoenthalpic (NpH), various Helmholtz energy derivatives in the NVE 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. Previous versions of this program (AEJF_v1_0 and AEJF_v2_0) may be found at http://dx.doi.org/10.1016/j.cpc.2011.04.026 and http://dx.doi.org/10.1016/j.cpc.2014.07.012, respectively.本研究介绍了分子模拟工具ms2（Deublein等，2011；Glass等，2014）的3.0版本更新。ms2 3.0版本新增两类系综，即微正则系综（microcanonical ensemble, NVE）与等压-等焓系综（isobaric-isoenthalpic ensemble, NpH）；新增功能还包括微正则系综下的多种亥姆霍兹自由能（Helmholtz energy）导数、用于计算化学势的热力学积分（thermodynamic integration）方法、用于计算溶剂活度的渗透压计算模块、四元混合物的六个麦克斯韦-斯特藩（Maxwell-Stefan）扩散系数、氢键采样统计数据、光滑粒子网格埃瓦尔德（smooth-particle mesh Ewald）求和算法，以及支持在单次程序运行中对任意数量的状态点执行分子动力学模拟。 该程序的过往版本（AEJF_v1_0与AEJF_v2_0）可分别通过以下链接获取：http://dx.doi.org/10.1016/j.cpc.2011.04.026 与 http://dx.doi.org/10.1016/j.cpc.2014.07.012。