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

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, i.e. 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

[1]  Roland Span,et al.  Multiparameter Equations of State: An Accurate Source of Thermodynamic Property Data , 2000 .

[2]  Hans Hasse,et al.  A set of molecular models for alkaline-earth cations in aqueous solution. , 2012, The journal of physical chemistry. B.

[3]  Jadran Vrabec,et al.  Lennard-Jones force field parameters for cyclic alkanes from cyclopropane to cyclohexane , 2015 .

[4]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[5]  Gábor Rutkai,et al.  Molecular simulation of the Joule–Thomson inversion curve of hydrogen sulphide , 2005 .

[6]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[7]  D. Frenkel,et al.  Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling. , 2007, The Journal of chemical physics.

[8]  Pengyu Y. Ren,et al.  Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .

[9]  Athanassios Z Panagiotopoulos,et al.  Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations. , 2015, The Journal of chemical physics.

[10]  Dirk Reith,et al.  GROW: A gradient-based optimization workflow for the automated development of molecular models , 2010, Comput. Phys. Commun..

[11]  Rolf Lustig,et al.  Direct molecular NVT simulation of the isobaric heat capacity, speed of sound and Joule–Thomson coefficient , 2011 .

[12]  Hans Hasse,et al.  A Set of Molecular Models for Symmetric Quadrupolar Fluids , 2001 .

[13]  Emanuele Paci,et al.  Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation. , 2011, Journal of chemical theory and computation.

[14]  David Chandler,et al.  Structure and hydrogen bond dynamics of water-dimethyl sulfoxide mixtures by computer simulations. Interim report, April 1992-October 1993 , 1993 .

[15]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[16]  Fernando A Escobedo,et al.  Thermodynamics and kinetics of bubble nucleation: simulation methodology. , 2012, The Journal of chemical physics.

[17]  Richard J. Sadus,et al.  Molecular simulation of the vapor–liquid coexistence of mercury , 2003 .

[18]  Hans Hasse,et al.  ms2: A molecular simulation tool for thermodynamic properties , 2011, Comput. Phys. Commun..

[19]  Yu. A. Chaikina.  Molecular Model for Critical Opalescence of Carbon Dioxide , 2018, Russian Journal of Physical Chemistry B.

[20]  W. Hamer,et al.  Osmotic Coefficients and Mean Activity Coefficients of Uni‐univalent Electrolytes in Water at 25°C , 1972 .

[21]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[22]  Yinyu Hu,et al.  Microscopic structure and interaction analysis for supercritical carbon dioxide-ethanol mixtures: a Monte Carlo simulation study. , 2009, The journal of physical chemistry. B.

[23]  M. G. Martin.  MCCCS Towhee: a tool for Monte Carlo molecular simulation , 2013 .

[24]  B. Widom,et al.  Some Topics in the Theory of Fluids , 1963 .

[25]  Amalendu Chandra,et al.  Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature. , 2006, The journal of physical chemistry. B.

[26]  Hans Hasse,et al.  Hydrogen bonding of methanol in supercritical CO2: comparison between 1H NMR spectroscopic data and molecular simulation results. , 2007, The journal of physical chemistry. B.

[27]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[28]  Elvira Guàrdia,et al.  Structure and Dynamics of Liquid Ethanol , 1997 .

[29]  Aman Sharma,et al.  Molecular simulation of shale gas adsorption and diffusion in inorganic nanopores , 2015 .

[30]  H. Hasse,et al.  Prediction of transport properties by molecular simulation: methanol and ethanol and their mixture. , 2008, The journal of physical chemistry. B.

[31]  D. Chandler,et al.  Hydrogen-bond kinetics in liquid water , 1996, Nature.

[32]  C. Vega,et al.  Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route. , 2016, The Journal of chemical physics.

[33]  Richard H. Henchman,et al.  Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water. , 2010, The journal of physical chemistry. B.

[34]  Michele Parrinello,et al.  Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states , 2003 .

[35]  Philippe Ungerer,et al.  Anisotropic united atom model including the electrostatic interactions of methylbenzenes. II. Transport properties , 2007 .

[36]  Hans Hasse,et al.  A set of molecular models for carbon monoxide and halogenated hydrocarbons , 2003 .

[37]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[38]  H. Hasse,et al.  Molecular dispersion energy parameters for alkali and halide ions in aqueous solution. , 2014, The Journal of chemical physics.

[39]  Hans Hasse,et al.  Automated development of force fields for the calculation of thermodynamic properties: acetonitrile as a case study , 2013 .

[40]  Amalendu Chandra,et al.  Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study. , 2014, The Journal of chemical physics.

[41]  Rolf Lustig,et al.  Statistical analogues for fundamental equation of state derivatives , 2012 .

[42]  George Jackson,et al.  Adsorption and separation of CO2/CH4 mixtures using nanoporous adsorbents by molecular simulation , 2014 .

[43]  Rolf Lustig,et al.  Microcanonical Monte Carlo simulation of thermodynamic properties , 1998 .

[44]  Hans Hasse,et al.  Density of Methanolic Alkali Halide Salt Solutions by Experiment and Molecular Simulation , 2015 .

[45]  Hans Hasse,et al.  Hydrogen bonding of ethanol in supercritical mixtures with CO2 by 1H NMR spectroscopy and molecular simulation , 2012 .

[46]  Jayant K. Singh,et al.  Structure and Dynamics of n-Alkanol Monolayers on a Mica Surface , 2014 .

[47]  Hans-Joachim Bungartz,et al.  Supercomputing for Molecular Dynamics Simulations , 2015, SpringerBriefs in Computer Science.

[48]  Roland Span,et al.  Equation of State for the Lennard-Jones Fluid , 2016 .

[49]  T. Cheatham,et al.  Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.

[50]  Rajamani Krishna,et al.  The Darken Relation for Multicomponent Diffusion in Liquid Mixtures of Linear Alkanes: An Investigation Using Molecular Dynamics (MD) Simulations , 2005 .

[51]  Peter T. Cummings,et al.  Phase Transitions of Water in Graphite and Mica Pores , 2011 .

[52]  Omar Matar,et al.  Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics. , 2016, ACS applied materials & interfaces.

[53]  P. Debenedetti,et al.  Recent advances in molecular simulation: A chemical engineering perspective , 2015 .

[54]  Jadran Vrabec,et al.  Mutual diffusion of binary liquid mixtures containing methanol, ethanol, acetone, benzene, cyclohexane, toluene, and carbon tetrachloride. , 2016, The Journal of chemical physics.

[55]  Hans Hasse,et al.  Vapor–liquid equilibria of hydrogen chloride, phosgene, benzene, chlorobenzene, ortho‐dichlorobenzene, and toluene by molecular simulation , 2011 .

[56]  Barbara Kirchner,et al.  Hydrogen bond detection. , 2006, The journal of physical chemistry. A.

[57]  Stefan Becker,et al.  ls1 mardyn: The massively parallel molecular dynamics code for large systems , 2014, Journal of chemical theory and computation.

[58]  Ivo Nezbeda,et al.  Molecular simulation of aqueous electrolytes: water chemical potential results and Gibbs-Duhem equation consistency tests. , 2013, The Journal of chemical physics.

[59]  Brian B. Laird,et al.  Molecular simulation of ethylene-expanded methanol: Phase behavior, structure, and transport properties , 2016 .

[60]  Mauro Ferrario,et al.  Molecular-dynamics simulation of liquid methanol , 1987 .

[61]  Hans Hasse,et al.  Molecular model for carbon dioxide optimized to vapor-liquid equilibria. , 2010, The Journal of chemical physics.

[62]  Martin T. Dove,et al.  DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism , 2006 .

[63]  Gábor Rutkai,et al.  Chemical potential calculations by thermodynamic integration with separation shifting in adaptive sampling Monte Carlo simulations , 2007 .

[64]  Jadran Vrabec,et al.  Vapor pressure of R227ea + ethanol at 343.13 K by molecular simulation , 2007 .

[65]  H. G. Petersen,et al.  Error estimates on averages of correlated data , 1989 .

[66]  Hans Hasse,et al.  Molecular simulation study of hydrogen bonding mixtures and new molecular models for mono- and dimethylamine , 2008 .

[67]  Hans Hasse,et al.  ms2: A molecular simulation tool for thermodynamic properties, new version release , 2014, Comput. Phys. Commun..

[68]  M Mezei,et al.  Free Energy Simulations a , 1986, Annals of the New York Academy of Sciences.

[69]  Dirk Reith,et al.  Assessment of numerical optimization algorithms for the development of molecular models , 2010, Comput. Phys. Commun..

[70]  Philippe Ungerer,et al.  Thermodynamic study of binary systems containing sulphur dioxide: Measurements and molecular modelling , 2011 .

[71]  David L Mobley,et al.  Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. , 2007, The Journal of chemical physics.

[72]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[73]  Hans Hasse,et al.  Molecular modelling and simulation of the surface tension of real quadrupolar fluids , 2014, ArXiv.

[74]  Colin W. Glass,et al.  Automatized determination of fundamental equations of state based on molecular simulations in the cloud , 2016 .

[75]  H. Hasse,et al.  Henry’s law constants of methane, nitrogen, oxygen and carbon dioxide in ethanol from 273 to 498 K: Prediction from molecular simulation , 2005, 0904.4793.

[76]  Ivo Nezbeda,et al.  Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields. , 2015, Journal of chemical theory and computation.

[77]  Hans Hasse,et al.  Multicriteria optimization of molecular force fields by Pareto approach , 2014 .

[78]  Daniel Staak,et al.  Fluid phase behavior from molecular simulation: Hydrazine, Monomethylhydrazine, Dimethylhydrazine and binary mixtures containing these compounds , 2012 .

[79]  Hans Hasse,et al.  Molecular model for formic acid adjusted to vapor–liquid equilibria , 2007 .

[80]  Daniel Staak,et al.  Molecular simulation of the vapor–liquid phase behavior of cyanides and their binary mixtures , 2013 .

[81]  Philippe Ungerer,et al.  Prediction of thermodynamic derivative properties of fluids by Monte Carlo simulation , 2001 .

[82]  Hans-Jörg Limbach,et al.  ESPResSo - an extensible simulation package for research on soft matter systems , 2006, Comput. Phys. Commun..

[83]  Hans Hasse,et al.  Molecular simulation study on the solubility of carbon dioxide in mixtures of cyclohexane + cyclohexanone , 2012 .

[84]  Hans Hasse,et al.  Solvent activity in electrolyte solutions from molecular simulation of the osmotic pressure. , 2016, The Journal of chemical physics.

[85]  David J. Nesbitt,et al.  Definition of the hydrogen bond (IUPAC Recommendations 2011) , 2011 .

[86]  Jadran Vrabec,et al.  Vapor–liquid equilibria of ethylene (C2H4) + decafluorobutane (C4F10) at 268–298 K from experiment, molecular simulation and the Peng–Robinson equation of state , 2012 .

[87]  Jeffrey J. Potoff,et al.  Development of an optimized intermolecular potential for sulfur dioxide. , 2011, The journal of physical chemistry. B.

[88]  Philippe Ungerer,et al.  Molecular simulation of the thermophysical properties of fluids: From understanding toward quantitative predictions , 2007 .