The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure.
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[1] Gregory A Voth,et al. The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.
[2] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[3] M Scott Shell,et al. Coarse-graining errors and numerical optimization using a relative entropy framework. , 2011, The Journal of chemical physics.
[4] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[5] Hyung Min Cho,et al. Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively. , 2009, The Journal of chemical physics.
[6] Gregory A. Voth,et al. The multiscale challenge for biomolecular systems: coarse-grained modeling , 2006 .
[7] Alexey Savelyev,et al. Chemically accurate coarse graining of double-stranded DNA , 2010, Proceedings of the National Academy of Sciences.
[8] Gregory A Voth,et al. Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation. , 2005, The journal of physical chemistry. B.
[9] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[10] Alexander Lyubartsev,et al. Systematic coarse-graining of molecular models by the Newton inversion method. , 2010, Faraday discussions.
[11] L. Larini,et al. A generalized mean field theory of coarse-graining. , 2010, The Journal of chemical physics.
[12] Sergei Izvekov,et al. The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials. , 2010, The Journal of chemical physics.
[13] Wataru Shinoda,et al. A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. , 2009, Journal of chemical theory and computation.
[14] Gregory A Voth,et al. Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.
[15] Alexander Lukyanov,et al. Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.
[16] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[17] Sergei Izvekov,et al. Towards an understanding of many-particle effects in hydrophobic association in methane solutions. , 2011, The Journal of chemical physics.
[18] S. Lifson,et al. Neighbor Interactions and Internal Rotations in Polymer Molecules. IV. Solvent Effect on Internal Rotations , 1960 .
[19] Hyung Min Cho,et al. Dissecting force interactions in cellulose deconstruction reveals the required solvent versatility for overcoming biomass recalcitrance. , 2011, Journal of the American Chemical Society.
[20] Hansen,et al. Can polymer coils Be modeled as "Soft colloids"? , 2000, Physical review letters.
[21] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[22] Ilpo Vattulainen,et al. Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. , 2009, The Journal of chemical physics.
[23] W G Noid,et al. Recovering physical potentials from a model protein databank , 2010, Proceedings of the National Academy of Sciences.
[24] Dirk Reith,et al. Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..
[25] J. Skolnick. In quest of an empirical potential for protein structure prediction. , 2006, Current opinion in structural biology.
[26] A. Liwo,et al. A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .
[27] Jocelyn M Rodgers,et al. Attraction between like-charged walls: Short-ranged simulations using local molecular field theory. , 2006, Physical review letters.
[28] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[29] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[30] P. B. Warren. Vapor-liquid coexistence in many-body dissipative particle dynamics. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[31] C. Panayiotou,et al. Volumetric properties of binary mixtures. 1. 2-Propanone + 2,2,4-trimethylpentane and n-heptane + ethanol mixtures , 1991 .
[32] Gregory A Voth,et al. Solvent-free lipid bilayer model using multiscale coarse-graining. , 2009, The journal of physical chemistry. B.
[33] 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.
[34] Kurt Kremer,et al. Multiscale simulation of soft matter systems. , 2010, Faraday discussions.
[35] A. A. Louis,et al. Accurate effective pair potentials for polymer solutions , 2000 .
[36] Gregory A Voth,et al. Multiscale coarse-graining of monosaccharides. , 2007, The journal of physical chemistry. B.
[37] Gregory A Voth,et al. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. , 2010, Journal of chemical theory and computation.
[38] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[39] W. Schommers,et al. Pair potentials in disordered many-particle systems: A study for liquid gallium , 1983 .
[40] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[41] Alexey Savelyev,et al. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. , 2009, Biophysical journal.
[42] S. Nosé. A molecular dynamics method for simulations in the canonical ensemble , 1984 .
[43] M. Klein,et al. Molecular dynamics simulations of surfactant self-organization at a solid-liquid interface. , 2006, Journal of the American Chemical Society.
[44] Avisek Das,et al. The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. , 2009, The Journal of chemical physics.
[45] Ilpo Vattulainen,et al. Multiscale modeling of emergent materials: biological and soft matter. , 2009, Physical chemistry chemical physics : PCCP.
[46] A. Liwo,et al. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field , 2001 .
[47] Kurt Kremer,et al. Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives , 2000 .
[48] R. C. Reeder,et al. A Coarse Grain Model for Phospholipid Simulations , 2001 .
[49] John D. Weeks,et al. Connecting Systems with Short and Long Ranged Interactions: Local Molecular Field Theory for Ionic Fluids† , 2004 .
[50] T. Darden,et al. The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods , 1993 .
[51] Joseph F Rudzinski,et al. Coarse-graining entropy, forces, and structures. , 2011, The Journal of chemical physics.
[52] W G Noid,et al. Generalized Yvon-Born-Green theory for molecular systems. , 2009, Physical review letters.
[53] Gregory A Voth,et al. A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.
[54] Gregory A Voth,et al. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. , 2008, The Journal of chemical physics.
[55] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[56] M. Parrinello,et al. Strain fluctuations and elastic constants , 1982 .
[57] William George Noid,et al. Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .
[58] Ilpo Vattulainen,et al. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case , 2011 .
[59] Avisek Das,et al. The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. , 2010, The Journal of chemical physics.
[60] M Scott Shell,et al. The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.
[61] Katie A. Maerzke,et al. Transferable potentials for phase equilibria-coarse-grain description for linear alkanes. , 2011, The journal of physical chemistry. B.
[62] Nicolae Goga,et al. Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. , 2010, Faraday discussions.
[63] Gregory A. Voth,et al. Systematic coarse-graining of a multicomponent lipid bilayer. , 2009, The journal of physical chemistry. B.
[64] Kurt Kremer,et al. Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations , 2006 .
[65] M. Betancourt,et al. Another look at the conditions for the extraction of protein knowledge‐based potentials , 2009, Proteins.
[66] Gregory A Voth,et al. Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.
[67] M Scott Shell,et al. Relative entropy as a universal metric for multiscale errors. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[68] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[69] D. Thirumalai,et al. Metastability of the folded states of globular proteins. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[70] Alan K. Soper,et al. Empirical potential Monte Carlo simulation of fluid structure , 1996 .
[71] 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.
[72] Florian Müller-Plathe,et al. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.
[73] Gregory A Voth,et al. The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials. , 2010, The Journal of chemical physics.
[74] Alexey Savelyev,et al. Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl. , 2009, The journal of physical chemistry. B.
[75] G. Voth,et al. Unique spatial heterogeneity in ionic liquids. , 2005, Journal of the American Chemical Society.
[76] William George Noid,et al. A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials† , 2010 .
[77] W G Noid,et al. Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration. , 2010, The Journal of chemical physics.
[78] Wataru Shinoda,et al. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .
[79] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[80] Joseph F. Rudzinski,et al. Generalized-Yvon-Born-Green model of toluene , 2011 .
[81] Alexander P. Lyubartsev,et al. OSMOTIC AND ACTIVITY COEFFICIENTS FROM EFFECTIVE POTENTIALS FOR HYDRATED IONS , 1997 .
[82] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[83] Gregory A Voth,et al. The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials. , 2011, The Journal of chemical physics.
[84] Cristiano L. Dias,et al. Three-dimensional "Mercedes-Benz" model for water. , 2009, The Journal of chemical physics.
[85] Gregory A Voth,et al. Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.
[86] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.