Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Julija Zavadlav; Manuel N. Melo; Siewert J. Marrink; Matej Praprotnik

doi:10.1063/1.4923008

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

The Journal of Chemical Physics ◽

10.1063/1.4923008 ◽

2015 ◽

Vol 142 (24) ◽

pp. 244118 ◽

Cited By ~ 37

Author(s):

Julija Zavadlav ◽

Manuel N. Melo ◽

Siewert J. Marrink ◽

Matej Praprotnik

Keyword(s):

Coarse Grained ◽

Adaptive Resolution ◽

Water Models ◽

Resolution Simulation

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Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion

Journal of Chemical Theory and Computation ◽

10.1021/ct3003354 ◽

2012 ◽

Vol 8 (8) ◽

pp. 2878-2887 ◽

Cited By ~ 51

Author(s):

Han Wang ◽

Christof Schütte ◽

Luigi Delle Site

Keyword(s):

Structural Transition ◽

Coarse Grained ◽

Adaptive Resolution ◽

Grand Canonical ◽

Resolution Simulation

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Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c09805 ◽

2021 ◽

Vol 125 (3) ◽

pp. 789-797

Author(s):

Ksenia Korshunova ◽

Paolo Carloni

Keyword(s):

Molecular Mechanics ◽

Coarse Grained ◽

Open Boundary ◽

Adaptive Resolution ◽

Resolution Scheme

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PSO-Assisted Development of New Transferable Coarse-Grained Water Models

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b10542 ◽

2018 ◽

Vol 122 (6) ◽

pp. 1958-1971 ◽

Cited By ~ 14

Author(s):

Karteek K. Bejagam ◽

Samrendra Singh ◽

Yaxin An ◽

Carter Berry ◽

Sanket A. Deshmukh

Keyword(s):

Coarse Grained ◽

Water Models

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

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.6b00536 ◽

2016 ◽

Vol 12 (8) ◽

pp. 4138-4145 ◽

Cited By ~ 23

Author(s):

Julija Zavadlav ◽

Siewert J. Marrink ◽

Matej Praprotnik

Keyword(s):

Adaptive Resolution ◽

Resolution Simulation

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Erratum: “Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties” [J. Chem. Phys. 142, 195101 (2015)]

The Journal of Chemical Physics ◽

10.1063/1.4975169 ◽

2017 ◽

Vol 146 (4) ◽

pp. 049901

Author(s):

Aoife C. Fogarty ◽

Raffaello Potestio ◽

Kurt Kremer

Keyword(s):

Hydration Shell ◽

Chem Phys ◽

Adaptive Resolution ◽

Dynamical Properties ◽

Resolution Simulation

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Exploring the utility of coarse-grained water models for computational studies of interfacial systems

Molecular Physics ◽

10.1080/00268976.2010.503197 ◽

2010 ◽

Vol 108 (15) ◽

pp. 2007-2020 ◽

Cited By ~ 40

Author(s):

Xibing He ◽

Wataru Shinoda ◽

Russell DeVane ◽

Michael L. Klein

Keyword(s):

Coarse Grained ◽

Computational Studies ◽

Water Models

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Computational efficiency and Amdahl’s law for the adaptive resolution simulation technique

Computer Physics Communications ◽

10.1016/j.cpc.2017.01.030 ◽

2017 ◽

Vol 215 ◽

pp. 20-25 ◽

Cited By ~ 4

Author(s):

Christoph Junghans ◽

Animesh Agarwal ◽

Luigi Delle Site

Keyword(s):

Computational Efficiency ◽

Simulation Technique ◽

Amdahl’S Law ◽

Adaptive Resolution ◽

Resolution Simulation

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Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models

The Journal of Physical Chemistry Letters ◽

10.1021/jz2006622 ◽

2011 ◽

Vol 2 (14) ◽

pp. 1794-1798 ◽

Cited By ~ 29

Author(s):

Zhe Wu ◽

Qiang Cui ◽

Arun Yethiraj

Keyword(s):

Driving Force ◽

Electrostatic Interactions ◽

Coarse Grained ◽

Hydrophobic Peptides ◽

Water Models

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Optimization problem and efficient partitioning algorithm for transitions to finer-scale models in adaptive resolution simulation of articulated biopolymers

Multibody System Dynamics ◽

10.1007/s11044-017-9603-6 ◽

2017 ◽

Vol 42 (1) ◽

pp. 97-117 ◽

Cited By ~ 1

Author(s):

Mohammad Poursina ◽

Kurt S. Anderson

Keyword(s):

Optimization Problem ◽

Adaptive Resolution ◽

Scale Models ◽

Partitioning Algorithm ◽

Resolution Simulation

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Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

Computer Physics Communications ◽

10.1016/j.cpc.2017.09.020 ◽

2018 ◽

Vol 222 ◽

pp. 94-101 ◽

Cited By ~ 13

Author(s):

Luigi Delle Site

Keyword(s):

Theoretical Framework ◽

Adaptive Resolution ◽

Grand Canonical ◽

Resolution Simulation

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