Coarse-grained molecular models of water: a review
暂无分享,去创建一个
[1] M Scott Shell,et al. Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy. , 2009, Physical chemistry chemical physics : PCCP.
[2] Ilpo Vattulainen,et al. Novel Methods in Soft Matter Simulations , 2013 .
[3] Clare McCabe,et al. On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties. , 2010, The journal of physical chemistry. B.
[4] Douglas Steinley,et al. K-means clustering: a half-century synthesis. , 2006, The British journal of mathematical and statistical psychology.
[5] Bertrand Guillot,et al. A reappraisal of what we have learnt during three decades of computer simulations on water , 2002 .
[6] A. J. Markvoort,et al. The CUMULUS coarse graining method: transferable potentials for water and solutes. , 2011, The journal of physical chemistry. B.
[7] 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.
[8] Zesheng Li,et al. An automatic coarse-graining and fine-graining simulation method: application on polyethylene. , 2006, The journal of physical chemistry. B.
[9] Y. Vorobjev,et al. Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH. , 2011, Advances in protein chemistry and structural biology.
[10] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[11] K. Dill,et al. Theory for the three-dimensional Mercedes-Benz model of water. , 2009, The Journal of chemical physics.
[12] Wataru Shinoda,et al. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .
[13] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[14] Ken A Dill,et al. Physical Modeling of Aqueous Solvation , 2011, Journal of statistical physics.
[15] Gregory A Voth,et al. Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation. , 2005, The journal of physical chemistry. B.
[16] Kurt Kremer,et al. Classical simulations from the atomistic to the mesoscale and back: coarse graining an liquid crystal. , 2008, Soft matter.
[17] Christine Peter,et al. Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions. , 2011, Journal of chemical theory and computation.
[18] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[19] C. McCabe,et al. A coarse-grained model for amorphous and crystalline fatty acids. , 2010, The Journal of chemical physics.
[20] D. Bedrov,et al. Multiscale Modeling of Poly(ethylene oxide)-Poly(propylene oxide)-Poly(ethylene oxide) Triblock Copolymer Micelles in Aqueous Solution. , 2006, Journal of chemical theory and computation.
[21] J. MacQueen. Some methods for classification and analysis of multivariate observations , 1967 .
[22] Alexander P. Lyubartsev,et al. Hierarchical multiscale modelling scheme from first principles to mesoscale , 2009 .
[23] S. Glotzer,et al. Coarse-grained force field for simulating polymer-tethered silsesquioxane self-assembly in solution. , 2007, The Journal of chemical physics.
[24] Valeria Molinero,et al. Structural transformation in supercooled water controls the crystallization rate of ice , 2011, Nature.
[25] Gregory A Voth,et al. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. , 2004, The Journal of chemical physics.
[26] Dirk Reith,et al. Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..
[27] Juan Elezgaray,et al. A systematic method to derive force fields for coarse-grained simulations of phospholipids , 2006, Comput. Phys. Commun..
[28] Daniel Borgis,et al. A semi‐implicit solvent model for the simulation of peptides and proteins , 2004, J. Comput. Chem..
[29] Valeria Molinero,et al. Water modeled as an intermediate element between carbon and silicon. , 2009, The journal of physical chemistry. B.
[30] Gregory A Voth,et al. Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.
[31] Gregory A Voth,et al. A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.
[32] Gregory A Voth,et al. Fast centroid molecular dynamics: a force-matching approach for the predetermination of the effective centroid forces. , 2005, The Journal of chemical physics.
[33] Gergely Tóth,et al. Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials , 2007, Journal of physics. Condensed matter : an Institute of Physics journal.
[34] H. L. Le Roy,et al. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability; Vol. IV , 1969 .
[35] Pablo D. Dans,et al. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? , 2010 .
[36] I. Nezbeda,et al. From realistic to simple models of associating fluids. II. Primitive models of ammonia, ethanol and models of water revisited , 2004 .
[37] Alexander P. Lyubartsev,et al. On the Reduction of Molecular Degrees of Freedom in Computer Simulations , 2004 .
[38] Wataru Shinoda,et al. Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. , 2010, The journal of physical chemistry. B.
[39] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[40] 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.
[41] Weber,et al. Computer simulation of local order in condensed phases of silicon. , 1985, Physical review. B, Condensed matter.
[42] Alexander P. Lyubartsev,et al. Multiscale modeling of lipids and lipid bilayers , 2005, European Biophysics Journal.
[43] Charles L Brooks,et al. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. , 2008, Physical chemistry chemical physics : PCCP.
[44] W F Drew Bennett,et al. Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining. , 2011, Journal of chemical theory and computation.
[45] Y. Guissani,et al. How to build a better pair potential for water , 2001 .
[46] Gregory A Voth,et al. Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method. , 2005, The journal of physical chemistry. B.
[47] T. Cheatham,et al. A coarse-grained model of DNA with explicit solvation by water and ions. , 2011, The journal of physical chemistry. B.
[48] Ken A. Dill,et al. A Simple Model of Water and the Hydrophobic Effect , 1998 .
[49] Daniel Borgis,et al. Particle-Based Implicit Solvent Model for Biosimulations: Application to Proteins and Nucleic Acids Hydration. , 2006, Journal of chemical theory and computation.
[50] J. Holt. Methods for probing water at the nanoscale , 2008 .
[51] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[52] C. McCabe,et al. A structurally relevant coarse-grained model for cholesterol. , 2010, Biophysical journal.
[53] George Malenkov. Liquid water and ices: understanding the structure and physical properties. , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[54] Daniel Borgis,et al. Combining a polarizable force‐field and a coarse‐grained polarizable solvent model. II. Accounting for hydrophobic effects , 2011, J. Comput. Chem..
[55] Eric Jakobsson,et al. A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes. , 2010, Journal of chemical theory and computation.
[56] I. Nezbeda,et al. Thermodynamics of simple models of associating fluids: primitive models of ammonia, methanol, ethanol and water , 2004 .
[57] Durba Sengupta,et al. Polarizable Water Model for the Coarse-Grained MARTINI Force Field , 2010, PLoS Comput. Biol..
[58] Siewert J Marrink,et al. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. , 2005, Chemistry and physics of lipids.
[59] Liam C. Jacobson,et al. Thermodynamic stability and growth of guest-free clathrate hydrates: a low-density crystal phase of water. , 2009, The journal of physical chemistry. B.
[60] Liam C. Jacobson,et al. A methane-water model for coarse-grained simulations of solutions and clathrate hydrates. , 2010, The journal of physical chemistry. B.
[61] Arun Yethiraj,et al. A new coarse-grained model for water: the importance of electrostatic interactions. , 2010, The journal of physical chemistry. B.
[62] Feng Wang,et al. Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions. , 2010, The Journal of chemical physics.
[63] Cristiano L. Dias,et al. Three-dimensional "Mercedes-Benz" model for water. , 2009, The Journal of chemical physics.
[64] Paulo A Netz,et al. Structural anomalies for a three dimensional isotropic core-softened potential. , 2006, The Journal of chemical physics.
[65] Alexander Lyubartsev,et al. Systematic coarse-graining of molecular models by the Newton inversion method. , 2010, Faraday discussions.
[66] M. Barbosa,et al. Thermodynamic and dynamic anomalies for a three-dimensional isotropic core-softened potential. , 2005, The Journal of chemical physics.
[67] Wilfred F van Gunsteren,et al. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. , 2011, The Journal of chemical physics.