Coarse‐grained models of water

Coarse‐grained (CG) models for macromolecules have become a standard in the study of biological systems, overcoming limitations in size and time scales encountered by atomistic molecular dynamics simulations. Just as in any biomolecular ensemble, water in CG models plays a key role in mediating intermolecular and intramolecular interactions. However, owing to the highly nontrivial properties of water, important simplifications have been commonly used to treat solvation effects. Recent developments of CG models for water are overviewed, comparing some characteristic features and limitations.

[1]  Wilfred F. van Gunsteren,et al.  Development of a simple, self-consistent polarizable model for liquid water , 2003 .

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

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

[4]  K. Dill,et al.  Theory for the three-dimensional Mercedes-Benz model of water. , 2009, The Journal of chemical physics.

[5]  Julien Michel,et al.  Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. , 2008, The journal of physical chemistry. B.

[6]  Joanna Trylska,et al.  Binding Pathways of Ligands to HIV‐1 Protease: Coarse‐grained and Atomistic Simulations , 2007, Chemical biology & drug design.

[7]  D. Chandler Interfaces and the driving force of hydrophobic assembly , 2005, Nature.

[8]  Adam Liwo,et al.  Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. , 2010, The journal of physical chemistry. A.

[9]  Arun Yethiraj,et al.  A new coarse-grained model for water: the importance of electrostatic interactions. , 2010, The journal of physical chemistry. B.

[10]  Wilfred F van Gunsteren,et al.  On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. , 2009, Physical chemistry chemical physics : PCCP.

[11]  Alexander D. MacKerell Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..

[12]  Carlos F. Lopez,et al.  Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation. , 2001, Biophysical journal.

[13]  M. Sansom,et al.  Coarse-grained simulation: a high-throughput computational approach to membrane proteins. , 2008, Biochemical Society transactions.

[14]  Michael L. Klein,et al.  Coarse grain models and the computer simulation of soft materials , 2004 .

[15]  Peter G. Kusalik,et al.  The Spatial Structure in Liquid Water , 1994, Science.

[16]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[17]  A polarizable coarse-grained water model for coarse-grained proteins simulations , 2009 .

[18]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[19]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[20]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[21]  V. Molinero,et al.  Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials. , 2009, The Journal of chemical physics.

[22]  Michele Parrinello,et al.  Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. , 2007, Journal of chemical theory and computation.

[23]  Role of short-range directional interactions in coarse-graining of protic/aprotic liquids. , 2009, The journal of physical chemistry. B.

[24]  Grace Brannigan,et al.  Solvent-free simulations of fluid membrane bilayers. , 2004, The Journal of chemical physics.

[25]  D. Schwartz,et al.  A coarse grain model for DNA. , 2007, The Journal of chemical physics.

[26]  Qiang Shi,et al.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. , 2006, The journal of physical chemistry. B.

[27]  Sergio Pantano,et al.  A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. , 2010, Journal of chemical theory and computation.

[28]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[29]  C. H. Walker The Hydrophobic Effect: Formation of Micelles and Biological Membranes , 1981 .

[30]  E. D. Cyan Handbook of Chemistry and Physics , 1970 .

[31]  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.

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

[33]  Daniel Borgis,et al.  A coarse-grained protein-protein potential derived from an all-atom force field. , 2007, The journal of physical chemistry. B.

[34]  Siewert J Marrink,et al.  Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. , 2011, Physical chemistry chemical physics : PCCP.

[35]  Krzysztof Szalewicz,et al.  Towards the complete understanding of water by a first-principles computational approach , 2009 .

[36]  B. Roux,et al.  Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions , 2010 .

[37]  Pablo D. Dans,et al.  Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? , 2010 .

[38]  G. Voth Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[39]  J. Essex,et al.  Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes , 2011, Journal of The Royal Society Interface.

[40]  B. Hess,et al.  Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models. , 2006, The journal of physical chemistry. B.

[41]  Ken A. Dill,et al.  A Simple Model of Water and the Hydrophobic Effect , 1998 .

[42]  Alexey Savelyev,et al.  Chemically accurate coarse graining of double-stranded DNA , 2010, Proceedings of the National Academy of Sciences.

[43]  Bin Chen,et al.  Liquid Water from First Principles: Investigation of Different Sampling Approaches , 2004 .

[44]  Siewert J Marrink,et al.  Martini Coarse-Grained Force Field: Extension to Carbohydrates. , 2009, Journal of chemical theory and computation.

[45]  M. Klein,et al.  Exploring the utility of coarse-grained water models for computational studies of interfacial systems , 2010 .

[46]  Klaus Schulten,et al.  Four-scale description of membrane sculpting by BAR domains. , 2008, Biophysical journal.

[47]  Bernd Ensing,et al.  Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. , 2010, Physical chemistry chemical physics : PCCP.

[48]  Pierre Tufféry,et al.  PEP-FOLD: an online resource for de novo peptide structure prediction , 2009, Nucleic Acids Res..

[49]  Toshiko Ichiye,et al.  Soft Sticky Dipole Potential for Liquid Water: A New Model , 1996 .

[50]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[51]  S. Pantano,et al.  A hybrid all-atom/coarse grain model for multiscale simulations of DNA. , 2011, Physical chemistry chemical physics : PCCP.

[52]  Valeria Molinero,et al.  Water modeled as an intermediate element between carbon and silicon. , 2009, The journal of physical chemistry. B.

[53]  Bertrand Guillot,et al.  A reappraisal of what we have learnt during three decades of computer simulations on water , 2002 .

[54]  Gregory C Rutledge,et al.  A novel algorithm for creating coarse-grained, density dependent implicit solvent models. , 2008, The Journal of chemical physics.

[55]  A. Wallqvist,et al.  Molecular Models of Water: Derivation and Description , 2007 .

[56]  Durba Sengupta,et al.  Polarizable Water Model for the Coarse-Grained MARTINI Force Field , 2010, PLoS Comput. Biol..

[57]  Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials. , 2005, The Journal of chemical physics.

[58]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[59]  Paul E. Smith,et al.  Simulated surface tensions of common water models. , 2007, The Journal of chemical physics.

[60]  Donald G Truhlar,et al.  Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations. , 2008, Journal of chemical theory and computation.

[61]  Wilfred F van Gunsteren,et al.  A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. , 2011, The Journal of chemical physics.

[62]  P. Derreumaux,et al.  HiRE-RNA: a high resolution coarse-grained energy model for RNA. , 2010, The journal of physical chemistry. B.