Preserving correlations between trajectories for efficient path sampling

Gingrich, Todd R.; Geissler, Phillip L.

doi:10.1063/1.4922343

Title: Preserving correlations between trajectories for efficient path sampling

Authors:

^[1]; Geissler, Phillip L. ^[2]

Department of Chemistry, University of California, Berkeley, California 94720, USA
Department of Chemistry, University of California, Berkeley, California 94720, USA, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

Publication Date:: Tue Jun 16 00:00:00 EDT 2015

Sponsoring Org.:: USDOE

OSTI Identifier:: 1228635

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: The Journal of Chemical Physics

Additional Journal Information:: Journal Name: The Journal of Chemical Physics Journal Volume: 142 Journal Issue: 23; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

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                    Gingrich, Todd R., and Geissler, Phillip L. Preserving correlations between trajectories for efficient path sampling.  United States: N. p., 2015. 
Web.  doi:10.1063/1.4922343.

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                    Gingrich, Todd R., & Geissler, Phillip L. Preserving correlations between trajectories for efficient path sampling.  United States.  https://doi.org/10.1063/1.4922343

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                    Gingrich, Todd R., and Geissler, Phillip L. Tue .  
"Preserving correlations between trajectories for efficient path sampling".  United States.  https://doi.org/10.1063/1.4922343.

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@article{osti_1228635,

  title        = {Preserving correlations between trajectories for efficient path sampling},

  author       = {Gingrich, Todd R. and Geissler, Phillip L.},

  abstractNote = {},

  doi          = {10.1063/1.4922343},

  journal      = {The Journal of Chemical Physics},

  number       = 23,

  volume       = 142,

  place        = {United States},

  year         = {Tue Jun 16 00:00:00 EDT 2015},

  month        = {Tue Jun 16 00:00:00 EDT 2015}

}

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Title: Preserving correlations between trajectories for efficient path sampling

Citation Formats

Stochastic thermodynamics, fluctuation theorems and molecular machines journal, November 2012

Precision shooting: Sampling long transition pathways journal, November 2008

Dynamic Order-Disorder in Atomistic Models of Structural Glass Formers journal, March 2009

Damage spreading in the Ising model journal, July 1997

Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids journal, June 1971

Biased Sampling of Nonequilibrium Trajectories: Can Fast Switching Simulations Outperform Conventional Free Energy Calculation Methods? † journal, April 2005

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies journal, September 2005

Steered transition path sampling journal, June 2012

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation journal, October 2011

T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark journal, October 2002

Exact Large Deviation Function in the Asymmetric Exclusion Process journal, January 1998

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems journal, March 2014

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT journal, March 2008

Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach journal, January 2008

Nonequilibrium Equality for Free Energy Differences journal, April 1997

Path sampling with stochastic dynamics: Some new algorithms journal, July 2007

High-precision work distributions for extreme nonequilibrium processes in large systems journal, May 2014

Reaction coordinates of biomolecular isomerization journal, May 2000

Comparative study of damage spreading in the Ising model using heat-bath, glauber, and metropolis dynamics journal, May 1990

Thermodynamic Formalism for Systems with Markov Dynamics journal, January 2007

First-order dynamical phase transition in models of glasses: an approach based on ensembles of histories journal, January 2009

Equation of State Calculations by Fast Computing Machines journal, June 1953

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality journal, August 2003

Homogeneous nucleation under shear in a two-dimensional Ising model: Cluster growth, coalescence, and breakup journal, October 2008

Measurement of nonequilibrium entropy from space-time thermodynamic integration journal, July 2008

Efficient transition path sampling for nonequilibrium stochastic dynamics journal, July 2001

Autoionization in Liquid Water journal, March 2001

Monte Carlo sampling methods using Markov chains and their applications journal, April 1970

Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality journal, June 2002

Stochastic thermodynamics, fluctuation theorems and molecular machines
journal, November 2012

Precision shooting: Sampling long transition pathways
journal, November 2008

Dynamic Order-Disorder in Atomistic Models of Structural Glass Formers
journal, March 2009

Damage spreading in the Ising model
journal, July 1997

Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids
journal, June 1971

Biased Sampling of Nonequilibrium Trajectories: Can Fast Switching Simulations Outperform Conventional Free Energy Calculation Methods? ^†
journal, April 2005

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
journal, September 2005

Steered transition path sampling
journal, June 2012

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
journal, October 2011

T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
journal, October 2002

Exact Large Deviation Function in the Asymmetric Exclusion Process
journal, January 1998

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
journal, March 2014

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT
journal, March 2008

Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach
journal, January 2008

Nonequilibrium Equality for Free Energy Differences
journal, April 1997

Path sampling with stochastic dynamics: Some new algorithms
journal, July 2007

High-precision work distributions for extreme nonequilibrium processes in large systems
journal, May 2014

Reaction coordinates of biomolecular isomerization
journal, May 2000

Comparative study of damage spreading in the Ising model using heat-bath, glauber, and metropolis dynamics
journal, May 1990

Thermodynamic Formalism for Systems with Markov Dynamics
journal, January 2007

First-order dynamical phase transition in models of glasses: an approach based on ensembles of histories
journal, January 2009

Equation of State Calculations by Fast Computing Machines
journal, June 1953

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
journal, August 2003

Homogeneous nucleation under shear in a two-dimensional Ising model: Cluster growth, coalescence, and breakup
journal, October 2008

Measurement of nonequilibrium entropy from space-time thermodynamic integration
journal, July 2008

Efficient transition path sampling for nonequilibrium stochastic dynamics
journal, July 2001

Autoionization in Liquid Water
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Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality
journal, June 2002