Systematic coarse-graining methods for soft matter simulations – a review (Q58820898)

1

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Elena A. Algaer

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Pritam Ganguly

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Chunli Li

4

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Francisco Rodríguez-Ropero

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Nico F. A. van der Vegt

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

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publication date

2013

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published in

Soft Matter

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volume

9

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issue

7

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page(s)

2108-2119

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cites work

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Adaptive multiscale molecular dynamics of macromolecular fluids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Deriving effective mesoscale potentials from atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Effective force coarse-graining

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The MARTINI force field: coarse grained model for biomolecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Transferable Potentials for Phase Equilibria−Coarse-Grain Description for Linear Alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Systematic methods for structurally consistent coarse-grained models

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-graining errors and numerical optimization using a relative entropy framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Multiscale coarse graining of liquid-state systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Coarse-graining entropy, forces, and structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Systematic coarse-graining of molecular models by the Newton inversion method

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Multiscale coarse-graining and structural correlations: connections to liquid-state theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

K-means clustering: a half-century synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

The search for the hydrophobic force law.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

How good are coarse-grained polymer models? A comparison for atactic polystyrene.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Interactions between macromolecules and ions: The Hofmeister series

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Multiscale approaches and perspectives to modeling aqueous electrolytes and polyelectrolytes

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Effective solvent mediated potentials of Na+ and Cl- ions in aqueous solution: temperature dependence

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Chemically accurate coarse graining of double-stranded DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2SM27201F