Literature DB >> 19198906

Comparative atomistic and coarse-grained study of water: what do we lose by coarse-graining?

Han Wang1, Christoph Junghans, Kurt Kremer.   

Abstract

We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the water clusters. It is shown that for simple two-body potentials either the radial distribution function or the geometrical packing can be optimized. In a similar way, as needed for multiscale methods, either the pressure or the compressibility can be fitted to the all atom liquid. In total, a speed-up by a factor of about 50 in computational time can be reached by this coarse-graining procedure.

Entities:  

Year:  2009        PMID: 19198906     DOI: 10.1140/epje/i2008-10413-5

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  12 in total

1.  Relationship between structural order and the anomalies of liquid water.

Authors:  J R Errington; P G Debenedetti
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3.  Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

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Journal:  J Chem Phys       Date:  2005-04-01       Impact factor: 3.488

4.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

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5.  Representability problems for coarse-grained water potentials.

Authors:  Margaret E Johnson; Teresa Head-Gordon; Ard A Louis
Journal:  J Chem Phys       Date:  2007-04-14       Impact factor: 3.488

6.  Limitations of the rigid planar nonpolarizable models of water.

Authors:  András Baranyai; Albert Bartók; Ariel A Chialvo
Journal:  J Chem Phys       Date:  2006-02-21       Impact factor: 3.488

7.  Simple and robust solver for the Poisson-Boltzmann equation.

Authors:  M Baptista; R Schmitz; B Dünweg
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-07-22

8.  Concurrent triple-scale simulation of molecular liquids.

Authors:  Rafael Delgado-Buscalioni; Kurt Kremer; Matej Praprotnik
Journal:  J Chem Phys       Date:  2008-03-21       Impact factor: 3.488

9.  Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials.

Authors:  Sergei Izvekov; Jessica M J Swanson; Gregory A Voth
Journal:  J Phys Chem B       Date:  2008-03-27       Impact factor: 2.991

10.  Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1995-10
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  17 in total

Review 1.  Computational studies of peptide-induced membrane pore formation.

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Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-08-05       Impact factor: 6.237

2.  A coarse-grained model for amorphous and crystalline fatty acids.

Authors:  K R Hadley; C McCabe
Journal:  J Chem Phys       Date:  2010-04-07       Impact factor: 3.488

3.  On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  J Phys Chem B       Date:  2010-04-08       Impact factor: 2.991

4.  Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.

Authors:  Jaehyeok Jin; Alexander J Pak; Gregory A Voth
Journal:  J Phys Chem Lett       Date:  2019-07-30       Impact factor: 6.475

5.  Coarse-Grained Molecular Models of Water: A Review.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  Mol Simul       Date:  2012-07-04       Impact factor: 2.178

6.  Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion.

Authors:  Timothy C Moore; Christopher R Iacovella; Clare McCabe
Journal:  Found Mol Model Simul (2015)       Date:  2016-06-02

7.  Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma.

Authors:  Na Zhang; Peng Zhang; Wei Kang; Danny Bluestein; Yuefan Deng
Journal:  J Comput Phys       Date:  2014-01-15       Impact factor: 3.553

8.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

Authors:  Jaehyeok Jin; Yining Han; Alexander J Pak; Gregory A Voth
Journal:  J Chem Phys       Date:  2021-01-28       Impact factor: 3.488

9.  Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.

Authors:  S Y Mashayak; Mara N Jochum; Konstantin Koschke; N R Aluru; Victor Rühle; Christoph Junghans
Journal:  PLoS One       Date:  2015-07-20       Impact factor: 3.240

10.  Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties.

Authors:  James L Suter; Derek Groen; Peter V Coveney
Journal:  Adv Mater       Date:  2014-12-09       Impact factor: 30.849

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