Evidence of information limitations in coarse-grained models.
暂无分享,去创建一个
[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.