Literature DB >> 26133421

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

Julija Zavadlav1, Manuel N Melo2, Siewert J Marrink2, Matej Praprotnik1.   

Abstract

Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 26133421     DOI: 10.1063/1.4923008

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

1.  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

Review 2.  SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.

Authors:  Julija Zavadlav; Siewert J Marrink; Matej Praprotnik
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 3.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 4.  Adaptive resolution simulations of biomolecular systems.

Authors:  Julija Zavadlav; Staš Bevc; Matej Praprotnik
Journal:  Eur Biophys J       Date:  2017-09-13       Impact factor: 1.733

5.  Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-03-15       Impact factor: 6.006

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.  Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.

Authors:  Julija Zavadlav; Siewert J Marrink; Matej Praprotnik
Journal:  J Chem Theory Comput       Date:  2016-07-25       Impact factor: 6.006

8.  Dual Resolution Membrane Simulations Using Virtual Sites.

Authors:  Yang Liu; Alex H De Vries; Jonathan Barnoud; Weria Pezeshkian; Josef Melcr; Siewert J Marrink
Journal:  J Phys Chem B       Date:  2020-05-01       Impact factor: 2.991

9.  Bayesian selection for coarse-grained models of liquid water.

Authors:  Julija Zavadlav; Georgios Arampatzis; Petros Koumoutsakos
Journal:  Sci Rep       Date:  2019-01-14       Impact factor: 4.379

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.