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

2012 ◽  
Vol 8 (8) ◽  
pp. 2878-2887 ◽  
Author(s):  
Han Wang ◽  
Christof Schütte ◽  
Luigi Delle Site
Keyword(s):  
Structural Transition ◽  
Coarse Grained ◽  
Adaptive Resolution ◽  
Grand Canonical ◽  
Resolution Simulation

scholarly journals Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

2015 ◽  
Vol 142 (24) ◽  
pp. 244118 ◽  
Author(s):  
Julija Zavadlav ◽  
Manuel N. Melo ◽  
Siewert J. Marrink ◽  
Matej Praprotnik
Keyword(s):  
Coarse Grained ◽  
Adaptive Resolution ◽  
Water Models ◽  
Resolution Simulation

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

2016 ◽  
Vol 12 (8) ◽  
pp. 4138-4145 ◽  
Author(s):  
Julija Zavadlav ◽  
Siewert J. Marrink ◽  
Matej Praprotnik
Keyword(s):  
Adaptive Resolution ◽  
Resolution Simulation

Free energies

2021 ◽  
pp. 139-178
Author(s):  
James P. Sethna
Keyword(s):  
Molecular Motors ◽  
Degrees Of Freedom ◽  
Reaction Rates ◽  
Coarse Grained ◽  
Rate Theory ◽  
Free Energies ◽  
Reaction Rate Theory ◽  
The World ◽  
The Cost ◽  
Grand Canonical

Free energies ignore most of a system, to provide the emergent statistical ensemble describing things we care about. Free energies can ignore the external world. The cost of borrowing energy from the world is measured by the temperature, giving us the canonical ensemble and Helmholtz free energy. Similarly, borrowing particles and volume from the world gives us the grand canonical and Gibbs ensembles. Free energies can ignore unimportant internal degrees of freedom. These lead to friction and noise, and theories of chemical reactions and reaction rates. Free energies can be coarse-grained, removing short distances and times. Exercises apply free energies to molecular motors, thermodynamic relations, reaction rate theory, Zipf’s law for word frequencies, zombie outbreaks, and nucleosynthesis.

Adaptive resolution simulation of oligonucleotides

2016 ◽  
Vol 145 (23) ◽  
pp. 234101 ◽  
Author(s):  
Paulo A. Netz ◽  
Raffaello Potestio ◽  
Kurt Kremer
Keyword(s):  
Adaptive Resolution ◽  
Resolution Simulation
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