Literature DB >> 21927736

Simulating water with rigid non-polarizable models: a general perspective.

Carlos Vega1, Jose L F Abascal.   

Abstract

Over the last forty years many computer simulations of water have been performed using rigid non-polarizable models. Since these models describe water interactions in an approximate way it is evident that they cannot reproduce all of the properties of water. By now many properties for these kinds of models have been determined and it seems useful to compile some of these results and provide a critical view of the successes and failures. In this paper a test is proposed in which 17 properties of water, from the vapour and liquid to the solid phases, are taken into account to evaluate the performance of a water model. A certain number of points between zero (bad agreement) and ten (good agreement) are given for the predictions of each model and property. We applied the test to five rigid non-polarizable models, TIP3P, TIP5P, TIP4P, SPC/E and TIP4P/2005, obtaining an average score of 2.7, 3.7, 4.7, 5.1, and 7.2 respectively. Thus although no model reproduces all properties, some models perform better than others. It is clear that there are limitations for rigid non-polarizable models. Neglecting polarizability prevents an accurate description of virial coefficients, vapour pressures, critical pressure and dielectric constant. Neglecting nuclear quantum effects prevents an accurate description of the structure, the properties of water below 120 K and the heat capacity. It is likely that for rigid non-polarizable models it may not be possible to increase the score in the test proposed here beyond 7.6. To get closer to experiment, incorporating polarization and nuclear quantum effects is absolutely required even though a substantial increase in computer time should be expected. The test proposed here, being quantitative and selecting properties from all phases of water can be useful in the future to identify progress in the modelling of water.

Entities:  

Year:  2011        PMID: 21927736     DOI: 10.1039/c1cp22168j

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  64 in total

1.  Direct calculation of ice homogeneous nucleation rate for a molecular model of water.

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Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-03       Impact factor: 11.205

2.  Molecular dynamics simulation of water permeation through the alpha-hemolysin channel.

Authors:  Jirasak Wong-Ekkabut; Mikko Karttunen
Journal:  J Biol Phys       Date:  2015-08-12       Impact factor: 1.365

3.  AMOEBA+ Classical Potential for Modeling Molecular Interactions.

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4.  Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.

Authors:  Julija Zavadlav; Jurij Sablić; Rudolf Podgornik; Matej Praprotnik
Journal:  Biophys J       Date:  2018-04-09       Impact factor: 4.033

5.  Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures.

Authors:  Ming-Liang Tan; Benjamin T Miller; Jerez Te; Joseph R Cendagorta; Bernard R Brooks; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2015-02-14       Impact factor: 3.488

Review 6.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

Review 7.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

8.  Membrane phase transition during heating and cooling: molecular insight into reversible melting.

Authors:  Liping Sun; Rainer A Böckmann
Journal:  Eur Biophys J       Date:  2017-07-19       Impact factor: 1.733

9.  Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

Authors:  Saeed Izadi; Boris Aguilar; Alexey V Onufriev
Journal:  J Chem Theory Comput       Date:  2015-08-21       Impact factor: 6.006

10.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
Journal:  J Chem Phys       Date:  2015-07-07       Impact factor: 3.488

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