Literature DB >> 31065343

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.

Julija Zavadlav1, Siewert J Marrink2, Matej Praprotnik3.   

Abstract

In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work.

Entities:  

Keywords:  adaptive resolution; molecular dynamics; supramolecular coupling

Year:  2019        PMID: 31065343      PMCID: PMC6501350          DOI: 10.1098/rsfs.2018.0075

Source DB:  PubMed          Journal:  Interface Focus        ISSN: 2042-8898            Impact factor:   3.906


  60 in total

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

Authors:  J R Errington; P G Debenedetti
Journal:  Nature       Date:  2001-01-18       Impact factor: 49.962

Review 2.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
Journal:  Nat Struct Biol       Date:  2002-09

3.  Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations.

Authors:  Thomas Soddemann; Burkhard Dünweg; Kurt Kremer
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-10-08

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

Authors:  Sergei Izvekov; Michele Parrinello; Christian J Burnham; Gregory A Voth
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

5.  Multiscale coarse graining of liquid-state systems.

Authors:  Sergei Izvekov; Gregory A Voth
Journal:  J Chem Phys       Date:  2005-10-01       Impact factor: 3.488

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

Authors:  Matej Praprotnik; Luigi Delle Site; Kurt Kremer
Journal:  J Chem Phys       Date:  2005-12-08       Impact factor: 3.488

7.  Concurrent dual-resolution Monte Carlo simulation of liquid methane.

Authors:  Cameron F Abrams
Journal:  J Chem Phys       Date:  2005-12-15       Impact factor: 3.488

8.  Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems.

Authors:  Igor V Pivkin; George E Karniadakis
Journal:  J Chem Phys       Date:  2006-05-14       Impact factor: 3.488

Review 9.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution.

Authors:  Matej Praprotnik; Luigi Delle Site; Kurt Kremer
Journal:  Annu Rev Phys Chem       Date:  2008       Impact factor: 12.703

10.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems.

Authors:  M Scott Shell
Journal:  J Chem Phys       Date:  2008-10-14       Impact factor: 3.488

View more
  1 in total

Review 1.  DPD Modelling of the Self- and Co-Assembly of Polymers and Polyelectrolytes in Aqueous Media: Impact on Polymer Science.

Authors:  Karel Procházka; Zuzana Limpouchová; Miroslav Štěpánek; Karel Šindelka; Martin Lísal
Journal:  Polymers (Basel)       Date:  2022-01-20       Impact factor: 4.329

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.