Literature DB >> 25591332

Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations.

Yunjie Chen1, Benoît Roux2.   

Abstract

A family of hybrid simulation methods that combines the advantages of Monte Carlo (MC) with the strengths of classical molecular dynamics (MD) consists in carrying out short non-equilibrium MD (neMD) trajectories to generate new configurations that are subsequently accepted or rejected via an MC process. In the simplest case where a deterministic dynamic propagator is used to generate the neMD trajectories, the familiar Metropolis acceptance criterion based on the change in the total energy ΔE, min[1, exp{-βΔE}], guarantees that the hybrid algorithm will yield the equilibrium Boltzmann distribution. However, the functional form of the acceptance probability is more complex when the non-equilibrium switching process is generated via a non-deterministic stochastic dissipative propagator coupled to a heat bath. Here, we clarify the conditions under which the Metropolis criterion remains valid to rigorously yield a proper equilibrium Boltzmann distribution within hybrid neMD-MC algorithm.

Mesh:

Year:  2015        PMID: 25591332     DOI: 10.1063/1.4904889

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


  9 in total

1.  Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture.

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Authors:  Yunjie Chen; Seyit Kale; Jonathan Weare; Aaron R Dinner; Benoît Roux
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4.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

5.  Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

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6.  Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

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Review 7.  Coupling structure with function in acid-sensing ion channels: challenges in pursuit of proton sensors.

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8.  Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.

Authors:  Yunjie Chen; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2015-08-11       Impact factor: 6.006

9.  Computer simulations of a heterogeneous membrane with enhanced sampling techniques.

Authors:  Yevhen K Cherniavskyi; Arman Fathizadeh; Ron Elber; D Peter Tieleman
Journal:  J Chem Phys       Date:  2020-10-14       Impact factor: 3.488

  9 in total

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