Evidence of information limitations in coarse-grained models.

Developing accurate coarse-grained (CG) models is critical for addressing long time and length scale phenomena with molecular simulations. Here, we distinguish and quantify two sources of error that are relevant to CG models in order to guide further methods development: "representability" errors, which result from the finite basis associated with the chosen functional form of the CG model and mapping operator, and "information" errors, which result from the limited kind and quantity of data supplied to the CG parameterization algorithm. We have performed a systematic investigation of these errors by generating all possible CG models of three liquids (butane, 1-butanol, and 1,3-propanediol) that conserve a set of chemically motivated locality and topology relationships. In turn, standard algorithms (iterative Boltzmann inversion, IBI, and multiscale coarse-graining, MSCG) were used to parameterize the models and the CG predictions were compared with atomistic results. For off-target properties, we observe a strong correlation between the accuracy and the resolution of the CG model, which suggests that the approximations represented by MSCG and IBI deteriorate with decreasing resolution. Conversely, on-target properties exhibit an extremely weak resolution dependence that suggests a limited role of representability errors in model accuracy. Taken together, these results suggest that simple CG models are capable of utilizing more information than is provided by standard parameterization algorithms, and that model accuracy can be improved by algorithm development rather than resorting to more complicated CG models.

[1]  Florian Müller-Plathe,et al.  Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains. , 2005, The journal of physical chemistry. B.

[2]  W G Noid,et al.  Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. , 2015, The Journal of chemical physics.

[3]  Gregory A Voth,et al.  Modeling real dynamics in the coarse-grained representation of condensed phase systems. , 2006, The Journal of chemical physics.

[4]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[5]  L. G. Leal,et al.  A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties. , 2012, The Journal of chemical physics.

[6]  Michael A Webb,et al.  Graph-Based Approach to Systematic Molecular Coarse-Graining. , 2019, Journal of chemical theory and computation.

[7]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.

[8]  Christoph Junghans,et al.  Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane , 2011 .

[9]  Pandurang M Kulkarni,et al.  A test of systematic coarse-graining of molecular dynamics simulations: Transport properties. , 2013, The Journal of chemical physics.

[10]  Kathryn M Lebold,et al.  Dual approach for effective potentials that accurately model structure and energetics. , 2019, The Journal of chemical physics.

[11]  Steven J. Plimpton,et al.  Implementing molecular dynamics on hybrid high performance computers - Particle-particle particle-mesh , 2012, Comput. Phys. Commun..

[12]  Gregory A Voth,et al.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.

[13]  Aleksander E. P. Durumeric,et al.  On the representability problem and the physical meaning of coarse-grained models. , 2016, The Journal of chemical physics.

[14]  Chenliang Xu,et al.  Encoding and selecting coarse-grain mapping operators with hierarchical graphs. , 2018, The Journal of chemical physics.

[15]  N. V. D. van der Vegt,et al.  Representability and Transferability of Kirkwood-Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems. , 2013, Journal of chemical theory and computation.

[16]  W G Noid,et al.  Generalized Yvon-Born-Green theory for molecular systems. , 2009, Physical review letters.

[17]  Pritam Ganguly,et al.  Convergence of Sampling Kirkwood-Buff Integrals of Aqueous Solutions with Molecular Dynamics Simulations. , 2013, Journal of chemical theory and computation.

[19]  Frank Neese,et al.  Software update: the ORCA program system, version 4.0 , 2018 .

[20]  Frank Noé,et al.  Machine Learning of Coarse-Grained Molecular Dynamics Force Fields , 2018, ACS central science.

[21]  Gregory A Voth,et al.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. , 2008, The Journal of chemical physics.

[22]  N. V. D. van der Vegt,et al.  Evaluation of mapping schemes for systematic coarse graining of higher alkanes. , 2017, Physical chemistry chemical physics : PCCP.

[23]  C. Adjiman,et al.  SAFT-γ force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes. , 2013, The journal of physical chemistry. B.

[24]  Katie A. Maerzke,et al.  Transferable potentials for phase equilibria-coarse-grain description for linear alkanes. , 2011, The journal of physical chemistry. B.

[25]  Gregory A Voth,et al.  Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.

[26]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[27]  D. Tieleman,et al.  Perspective on the Martini model. , 2013, Chemical Society reviews.

[28]  Michael A Webb,et al.  Enhancing Cation Diffusion and Suppressing Anion Diffusion via Lewis-Acidic Polymer Electrolytes. , 2016, The journal of physical chemistry letters.

[29]  Avisek Das,et al.  The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. , 2010, The Journal of chemical physics.

[30]  K. Binder,et al.  Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment. , 2008, The Journal of chemical physics.

[31]  Margaret E. Johnson,et al.  Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.

[32]  Kurt Kremer,et al.  Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? , 2009, The European physical journal. E, Soft matter.

[33]  Helgi I Ingólfsson,et al.  The power of coarse graining in biomolecular simulations , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[34]  Dirk Reith,et al.  Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..

[35]  A. Louis Beware of density dependent pair potentials , 2002, cond-mat/0205110.

[36]  A. Lyubartsev,et al.  Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[37]  Kurt Kremer,et al.  Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene , 2007 .

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

[39]  M. Klein,et al.  Constant pressure molecular dynamics algorithms , 1994 .

[40]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[41]  Janna K. Maranas,et al.  Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers. , 2011, The Journal of chemical physics.

[42]  Clare McCabe,et al.  Coarse-grained molecular models of water: a review , 2012, Molecular simulation.

[43]  D. Andrienko,et al.  Comparison of systematic coarse-graining strategies for soluble conjugated polymers , 2016 .

[44]  Wataru Shinoda,et al.  Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .

[45]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[46]  Gregory A Voth,et al.  The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials. , 2010, The Journal of chemical physics.

[47]  R. L. Henderson A uniqueness theorem for fluid pair correlation functions , 1974 .

[48]  Sanket A. Deshmukh,et al.  Development of New Transferable Coarse-Grained Models of Hydrocarbons. , 2018, The journal of physical chemistry. B.

[49]  Salvatore Torquato,et al.  Statistical mechanical models with effective potentials: Definitions, applications, and thermodynamic consequences , 2002 .

[50]  Alexander J. Pak,et al.  Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. , 2019, The journal of physical chemistry letters.

[51]  M Scott Shell,et al.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.