Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

1Department of Chemical and Biomolecular Engineering, The University of Notre Dame; 2Thermodynamics Research Center, National Institute of Standards and Technology; 3Chemical Engineering Department, Brigham Young University; 4Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health; 5Department of Chemical and Biomolecular Engineering, The University of Akron

[1]  G. Karniadakis,et al.  Nature of intrinsic uncertainties in equilibrium molecular dynamics estimation of shear viscosity for simple and complex fluids. , 2018, The Journal of chemical physics.

[2]  L. Vega,et al.  Transport properties of the ionic liquid 1-ethyl-3-methylimidazolium chloride from equilibrium molecular dynamics simulation. The effect of temperature. , 2006, The journal of physical chemistry. B.

[3]  Gerhard Hummer,et al.  System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions , 2004 .

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

[5]  David Hinkley,et al.  Bootstrap Methods: Another Look at the Jackknife , 2008 .

[6]  Michael G. Lerner,et al.  Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. , 2015, The Journal of chemical physics.

[7]  P. Daivis,et al.  Transport coefficients of liquid butane near the boiling point by equilibrium molecular dynamics , 1995 .

[8]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

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

[10]  Hans Hasse,et al.  ms2: A molecular simulation tool for thermodynamic properties, release 3.0 , 2017, Comput. Phys. Commun..

[11]  Berend Smit,et al.  Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities? , 2009, The Journal of chemical physics.

[12]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[13]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[14]  V. Stegailov,et al.  Rheology of liquid n-triacontane: Molecular dynamics simulation , 2016 .

[15]  E. Maginn,et al.  Thermal and Transport Properties of Six Ionic Liquids: An Experimental and Molecular Dynamics Study , 2012 .

[16]  Helgi I. Ingólfsson,et al.  Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. , 2017, The journal of physical chemistry. B.

[17]  S. Nosé A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[18]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[19]  F. Stillinger,et al.  Improved simulation of liquid water by molecular dynamics , 1974 .

[20]  G. Grest,et al.  Viscosity calculations of n-alkanes by equilibrium molecular dynamics , 1997 .

[21]  K. Refson,et al.  Viscosity and stress autocorrelation function in supercooled water: a molecular dynamics study , 2002 .

[22]  B. Hess Determining the shear viscosity of model liquids from molecular dynamics simulations , 2002 .

[23]  H. Hasse,et al.  Shear viscosity and thermal conductivity of quadrupolar real fluids from molecular simulation , 2005 .

[24]  Edward J Maginn,et al.  System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ethers. , 2016, The Journal of chemical physics.

[25]  T. Ohara,et al.  Hydrodynamic consideration of the finite size effect on the self-diffusion coefficient in a periodic rectangular parallelepiped system. , 2015, The Journal of chemical physics.

[26]  M. Shirts,et al.  Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations. , 2013, Journal of chemical theory and computation.

[27]  O. Borodin,et al.  Viscosity of a room temperature ionic liquid: predictions from nonequilibrium and equilibrium molecular dynamics simulations. , 2009, Journal of Physical Chemistry B.

[28]  Akihito Otani,et al.  Reliable Viscosity Calculation from Equilibrium Molecular Dynamics Simulations: A Time Decomposition Method. , 2015, Journal of chemical theory and computation.

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

[30]  Huai Sun,et al.  On the prediction of transport properties of ionic liquid using 1-n-butylmethylpyridinium tetrafluoroborate as an example , 2017 .

[31]  R. Prosmiti,et al.  Determining the bulk viscosity of rigid water models. , 2012, The journal of physical chemistry. A.

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

[33]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[34]  R. Cracknell,et al.  Shear viscosity of linear alkanes through molecular simulations: quantitative tests for n-decane and n-hexadecane , 2012 .

[35]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[36]  J. Ilja Siepmann,et al.  Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes , 1998 .

[37]  David van der Spoel,et al.  The Origin of Layer Structure Artifacts in Simulations of Liquid Water. , 2006, Journal of chemical theory and computation.

[38]  Thomas J Lane,et al.  MDTraj: a modern, open library for the analysis of molecular dynamics trajectories , 2014, bioRxiv.

[39]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[40]  W. C. Swope,et al.  A computer simulation method for the calculation of equilibrium constants for the formation of physi , 1981 .

[41]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[42]  Berk Hess,et al.  P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.

[43]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[44]  P. Rotureau,et al.  A General Guidebook for the Theoretical Prediction of Physicochemical Properties of Chemicals for Regulatory Purposes. , 2015, Chemical reviews.

[45]  H. Berendsen,et al.  A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field , 1998 .

[46]  P. Daivis,et al.  Comparison of constant pressure and constant volume nonequilibrium simulations of sheared model decane , 1994 .