1,878
Views
121
CrossRef citations to date
0
Altmetric
Original Articles

Coarse-grained molecular models of water: a review

&
Pages 671-681 | Received 23 Jan 2012, Accepted 27 Feb 2012, Published online: 04 Jul 2012

References

  • Guillot , B. 2002 . A reappraisal of what we have learnt during three decades of computer simulations on water . J. Mol. Liq. , 101 : 219 – 260 .
  • Holt , J.K. 2008 . Methods for probing water at the nanoscale . Microfluid. Nanofluid. , 5 : 425 – 442 .
  • Malenkov , G. 2009 . Liquid water and ices: Understanding the structure and physical properties . J. Phys. Condens, Matter , 21 283101 (35 pp.)
  • Guillot , B. and Guissani , Y. 2001 . How to build a better pair potential for water . J. Chem. Phys. , 114 : 6720 – 6733 .
  • Chen , J. and Brooks , C.L. III . 2008 . Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions . PCCP , 10 : 471 – 481 .
  • Fennell , C.J. and Dill , K.A. 2011 . Physical modeling of aqueous solvation . J. Stat. Phys. , 145 : 209 – 226 .
  • Vorobjev , Y.N. 2011 . “ Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant PH ” . In Advances in Protein Chemistry and Structural Biology, Vol 85: Computational Chemistry Methods in Structural Biology , Edited by: Christov , C. 281 – 322 . Waltham, MA : Elsevier, Inc. .
  • Shen , J.W. , Li , C.L. , van der Vegt , N.F.A. and Peter , C. 2011 . Transferability of coarse grained potentials: Implicit solvent models for hydrated ions . J. Chem. Theor. Comput. , 7 : 1916 – 1927 .
  • Hadley , K.R. and McCabe , C. 2010 . Developing a coarse-grained water model: Efficient mapping of multiple waters to a single site . J. Phys. Chem. B , 114 : 4590 – 4599 .
  • van Hoof , B. , Markvoort , A.J. , van Santen , R.A. and Hilbers , P.A.J. 2011 . The CUMULUS coarse graining method: Transferable potentials for water and solutes . J. Phys. Chem. B , 115 : 10001 – 10012 .
  • Izvekov , S. and Voth , G.A. 2005 . A multiscale coarse-graining method for biomolecular systems . J. Phys. Chem. B , 109 : 2469 – 2473 .
  • Toth , G. 2007 . Effective potentials from complex simulations: A potential-matching algorithm and remarks on coarse-grained potentials . J. Phys. Condens. Matter , 19 335222 (12 pp.)
  • Hone , T.D. , Izvekov , S. and Voth , G.A. 2005 . Fast centroid molecular dynamics: A force-matching approach for the predetermination of the effective centroid forces . J. Chem. Phys. , 122 054105 (7 pp.)
  • Izvekov , S. , Parrinello , M. , Burnham , C.J. and Voth , G.A. 2004 . Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching . J. Chem. Phys. , 120 : 10896 – 10913 .
  • Izvekov , S. , Violi , A. and Voth , G.A. 2005 . Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation . J. Phys. Chem. B , 109 : 17019 – 17024 .
  • Izvekov , S. and Voth , G.A. 2005 . Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method . J. Phys. Chem. B , 109 : 6573 – 6586 .
  • Izvekov , S. and Voth , G.A. 2005 . Multiscale coarse graining of liquid-state systems . J. Chem. Phys. , 123 134105 (13 pp.)
  • Lyubartsev , A.P. and Laaksonen , A. 1995 . Calculation of effective interaction potentials from radial-distribution functions – a reverse Monte-Carlo approach . Phys. Rev. E , 52 : 3730 – 3737 .
  • Lyubartsev , A.P. 2005 . Multiscale modeling of lipids and lipid bilayers . Eur. Biophys. J. Biophys. Lett. , 35 : 53 – 61 .
  • Lyubartsev , A. , Tu , Y.Q. and Laaksonen , A. 2009 . Hierarchical multiscale modelling scheme from first principles to mesoscale . J. Comput. Theor. Nanosci. , 6 : 951 – 959 .
  • Lyubartsev , A. , Mirzoev , A. , Chen , L.J. and Laaksonen , A. 2010 . Systematic coarse-graining of molecular models by the Newton inversion method . Faraday Discuss. , 144 : 43 – 56 .
  • Reith , D. , Putz , M. and Muller-Plathe , F. 2003 . Deriving effective mesoscale potentials from atomistic simulations . J. Comput. Chem. , 24 : 1624 – 1636 .
  • Elezgaray , J. and Laguerre , M. 2006 . A systematic method to derive force fields for coarse-grained simulations of phospholipids . Comput. Phys. Commun. , 175 : 264 – 268 .
  • Chen , L.J. , Qian , H.J. , Lu , Z.Y. , Li , Z.S. and Sun , C.C. 2006 . An automatic coarse-graining and fine-graining simulation method: Application on polyethylene . J. Phys. Chem. B , 110 : 24093 – 24100 .
  • Chan , E.R. , Striolo , A. , McCabe , C. , Cummings , P.T. and Glotzer , S.C. 2007 . Coarse-grained force field for simulating polymer-tethered silsesquioxane self-assembly in solution . J. Chem. Phys. , 127 114102 (14 pp.)
  • Peter , C. , Delle Site , L. and Kremer , K. 2008 . Classical simulations from the atomistic to the mesoscale and back: Coarse graining an azobenzene liquid crystal . Soft Matter , 4 : 859 – 869 .
  • Hadley , K.R. and McCabe , C. 2010 . Coarse-grained models for amorphous and crystalline fatty acids . J. Chem. Phys. , 132 : 134505 (11 pp.)
  • Hadley , K.R. and McCabe , C. 2010 . A structurally relevant coarse-grained model of cholesterol . Biophys. J. , 99 : 2896 – 2905 .
  • Hadley , K.R. and McCabe , C. 2012 . Self-assembly of coarse-grained skin lipids into an experimentally observed bilayer . DOI: 10.1039/C2SM07204A
  • Chan , E.R. , Striolo , A. , McCabe , C. , Glotzer , S.C. and Cummings , P.T. 2008 . “ A coarse-grained force field for simulating polymer-tethered nanoparticle self-assembly in solution ” . In Coarse-Graining of Condensed Phase and Biomolecular Systems , Edited by: Voth , G.A. Boca Raton, FL : Taylor & Francis .
  • Wei , D. and Wang , F. 2010 . Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions . J. Chem. Phys. , 133 084101 (6 pp.)
  • Lyubartsev , A.P. and Laaksonen , A. 2004 . “ On the reduction of molecular degrees of freedom in computer simulations ” . In Novel Methods in Soft Matter Simulations , Edited by: Karttunen , M. , Vattulainen , I. and Lukkarinen , A. 219 – 244 . Berlin : Springer-Verlag .
  • Bedrov , D. , Ayyagari , C. and Smith , G.D. 2006 . Multiscale modeling of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer micelles in aqueous solution . J. Chem. Theor. Comput. , 2 : 598 – 606 .
  • Wang , H. , Junghans , C. and Kremer , K. 2009 . Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? . Eur. Phys. J.E , 28 : 221 – 229 .
  • Berendsen , H.J.C. , Postma , J.P.M. , von Gunsteren , W.F. and Hermans , J. 1981 . “ Interaction models for water in relation to protein hydration ” . In Intermolecular Forces: Proceedings of the Fourteenth Jerusalem Symposium on Quantum Chemistry and Biochemistry , Edited by: Pullman , B. 331 – 342 . Dordrecht : Reidel .
  • Berendsen , H.J.C. , Grigera , J.R. and Straatsma , T.P. 1987 . The missing term in effective pair potentials . J. Phys. Chem. B , 91 : 6269 – 6271 .
  • Jorgensen , W.L. , Chandrasekhar , J. , Madura , J.D. , Impey , R.W. and Klein , M.L. 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926 – 935 .
  • Basdevant , N. , Borgis , D. and Ha-Duong , T. 2004 . A semi-implicit solvent model for the simulation of peptides and proteins . J. Comput. Chem. , 25 : 1015 – 1029 .
  • Basdevant , N. , Ha-Duong , T. and Borgis , D. 2006 . Particle-based implicit solvent model for biosimulations: Application to proteins and nucleic acids hydration . J. Chem. Theor. Comput. , 2 : 1646 – 1656 .
  • Masella , M. , Borgis , D. and Cuniasse , P. 2011 . Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects . J. Comput. Chem. , 32 : 2664 – 2678 .
  • Vlcek , L. and Nezbeda , I. 2004 . Thermodynamics of simple models of associating fluids: Primitive models of ammonia, methanol, ethanol and water . Mol. Phys. , 102 : 771 – 781 .
  • Vlcek , L. and Nezbeda , I. 2004 . From realistic to simple models of associating fluids. II. Primitive models of ammonia, ethanol and models of water revisited . Mol. Phys. , 102 : 485 – 497 .
  • Silverstein , K.A.T. , Haymet , A.D.J. and Dill , K.A. 1998 . A simple model of water and the hydrophobic effect . J. Am. Chem. Soc. , 120 : 3166 – 3175 .
  • Bizjak , A. , Urbi , T. , Vlachy , V. and Dill , K.A. 2007 . The three-dimensional “Mercedes Benz” model of water . Acta Chim. Slov. , 54 : 532 – 537 .
  • Bizjak , A. , Urbic , T. , Vlachy , V. and Dill , K.A. 2009 . Theory for the three-dimensional Mercedes-Benz model of water . J. Chem. Phys. , 131
  • Stillinger , F.H. and Weber , T.A. 1985 . Computer-simulation of local order in condensed phases of silicon . Phys. Rev. B , 31 : 5262 – 5271 .
  • Molinero , V. and Moore , E.B. 2009 . Water modeled as an intermediate element between carbon and silicon . J. Phys. Chem. B , 113 : 4008 – 4016 .
  • DeMille , R.C. , Cheatham , T.E. and Molinero , V. 2011 . A coarse-grained model of DNA with explicit solvation by water and ions . J. Phys. Chem. B , 115 : 132 – 142 .
  • Moore , E.B. and Molinero , V. 2011 . Structural transformation in supercooled water controls the crystallization rate of ice . Nature , 479 : 506 – 509 .
  • Jacobson , L.C. , Hujo , W. and Molinero , V. 2009 . Thermodynamic stability and growth of guest-free clathrate hydrates: A low-density crystal phase of water . J. Phys. Chem. B , 113 : 10298 – 10307 .
  • Jacobson , L.C. and Molinero , V. 2010 . A methane-water model for coarse-grained simulations of solutions and clathrate hydrates . J. Phys. Chem. B , 114 : 7302 – 7311 .
  • de Oliveira , A.B. , Netz , P.A. , Colla , T. and Barbosa , M.C. 2006 . Structural anomalies for a three dimensional isotropic core-softened potential . J. Chem. Phys. , 125 124503 (7 pp.)
  • de Oliveira , A.B. , Netz , P.A. , Colla , T. and Barbosa , M.C. 2006 . Thermodynamic and dynamic anomalies for a three-dimensional isotropic core-softened potential . J. Chem. Phys. , 124 084505 (6 pp.)
  • Chaimovich , A. and Shell , M.S. 2009 . Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy . PCCP , 11 : 1901 – 1915 .
  • MacQueen , J.B. 1967 . Some Methods for Classification and Analysis of Multivariate Observations , 5th Berkeley Symposium on Mathematical Statistics and Probability 281 – 297 . Berkeley, CA : University of California Press .
  • Steinley , D. 2006 . K-means clustering: A half-century synthesis . Br. J. Math. Stat. Psychol. , 59 : 1 – 34 .
  • Marrink , S.J. , de Vries , A.H. and Mark , A.E. 2004 . Coarse grained model for semiquantitative lipid simulations . J. Phys. Chem. B , 108 : 750 – 760 .
  • Marrink , S.J. , Risselada , J. and Mark , A.E. 2005 . Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model . Chem. Phys. Lipids , 135 : 223 – 244 .
  • Marrink , S.J. , Risselada , H.J. , Yefimov , S. , Tieleman , D.P. and de Vries , A.H. 2007 . The MARTINI force field: Coarse grained model for biomolecular simulations . J. Phys. Chem. B , 111 : 7812 – 7824 .
  • Chiu , S.-W. , Scott , H.L. and Jakobsson , E. 2010 . A coarse-grained model based on morse potential for water and n-alkanes . J. Chem. Theor. Comput. , 6 : 851 – 863 .
  • Shinoda , W. , Devane , R. and Klein , M.L. 2007 . Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants . Mol. Simul. , 33 : 27 – 36 .
  • Shinoda , W. , DeVane , R. and Klein , M.L. 2010 . Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field . J. Phys. Chem. B , 114 : 6836 – 6849 .
  • Yesylevskyy , S.O. , Schafer , L.V. , Sengupta , D. and Marrink , S.J. 2010 . Polarizable water model for the coarse-grained MARTINI force field . PLoS Comput. Biol. , 6 e1000810 (6 pp.)
  • Wu , Z. , Cui , Q. and Yethiraj , A. 2010 . A new coarse-grained model for water: The importance of electrostatic interactions . J. Phys. Chem. B , 114 : 10524 – 10529 .
  • Bennett , W.F.D. and Tieleman , D.P. 2011 . Water defect and pore formation in atomistic and coarse-grained lipid membranes: Pushing the limits of coarse graining . J. Chem. Theor. Comput. , 7 : 2981 – 2988 .
  • Darre , L. , Machado , M.R. , Dans , P.D. , Herrera , F.E. and Pantano , S. 2010 . Another coarse grain model for aqueous solvation: WAT FOUR? . J. Chem. Theor. Comput. , 6 : 3793 – 3807 .
  • Riniker , S. and van Gunsteren , W.F. 2011 . A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations . J. Chem. Phys. , 134 084110 (12 pp.)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.