Literature DB >> 32483559

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

Timothy C Moore1,2, Christopher R Iacovella1,2, Clare McCabe1,2,3.   

Abstract

A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.

Entities:  

Keywords:  crystallization; interface; pressure; surface tension

Year:  2016        PMID: 32483559      PMCID: PMC7262820          DOI: 10.1007/978-981-10-1128-3_3

Source DB:  PubMed          Journal:  Found Mol Model Simul (2015)


  25 in total

1.  Unique spatial heterogeneity in ionic liquids.

Authors:  Yanting Wang; Gregory A Voth
Journal:  J Am Chem Soc       Date:  2005-09-07       Impact factor: 15.419

2.  The MARTINI force field: coarse grained model for biomolecular simulations.

Authors:  Siewert J Marrink; H Jelger Risselada; Serge Yefimov; D Peter Tieleman; Alex H de Vries
Journal:  J Phys Chem B       Date:  2007-06-15       Impact factor: 2.991

3.  Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects.

Authors:  Michel Masella; Daniel Borgis; Philippe Cuniasse
Journal:  J Comput Chem       Date:  2011-06-06       Impact factor: 3.376

4.  Adaptive resolution simulation of polarizable supramolecular coarse-grained water models.

Authors:  Julija Zavadlav; Manuel N Melo; Siewert J Marrink; Matej Praprotnik
Journal:  J Chem Phys       Date:  2015-06-28       Impact factor: 3.488

5.  Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion.

Authors:  Timothy C Moore; Christopher R Iacovella; Clare McCabe
Journal:  J Chem Phys       Date:  2014-06-14       Impact factor: 3.488

6.  Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures.

Authors:  Hwankyu Lee; Richard W Pastor
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

7.  A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.

Authors:  See-Wing Chiu; H Larry Scott; Eric Jakobsson
Journal:  J Chem Theory Comput       Date:  2010-02-17       Impact factor: 6.006

8.  Polarizable water model for the coarse-grained MARTINI force field.

Authors:  Semen O Yesylevskyy; Lars V Schäfer; Durba Sengupta; Siewert J Marrink
Journal:  PLoS Comput Biol       Date:  2010-06-10       Impact factor: 4.475

9.  A semi-implicit solvent model for the simulation of peptides and proteins.

Authors:  Nathalie Basdevant; Daniel Borgis; Tap Ha-Duong
Journal:  J Comput Chem       Date:  2004-06       Impact factor: 3.376

10.  Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics.

Authors:  Goundla Srinivas; Dennis E Discher; Michael L Klein
Journal:  Nat Mater       Date:  2004-08-08       Impact factor: 43.841

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  2 in total

1.  Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition.

Authors:  Parashara Shamaprasad; Timothy C Moore; Donna Xia; Christopher R Iacovella; Annette L Bunge; Clare McCabe
Journal:  Langmuir       Date:  2022-06-07       Impact factor: 4.331

Review 2.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

  2 in total

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