Towards an optimal flow: Density-of-states-informed replica-exchange simulations

Vogel, Thomas; Perez, Danny

doi:10.1103/PhysRevLett.115.190602

Title: Towards an optimal flow: Density-of-states-informed replica-exchange simulations

Abstract

Here we learn that replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around phase transitions, or when a few hard-to-find configurations dominate the statistical averages. We introduce a generalized RE scheme, density-of-states-informed RE, that addresses some of these challenges. The key feature of our approach is to inform the simulation with readily available, but commonly unused, information on the density of states of the system as the RE simulation proceeds. This enables two improvements, namely, the introduction of resampling moves that actively move the system towards equilibrium and the continual adaptation of the optimal temperature set. As a consequence of these two innovations, we show that the configuration flow in temperature space is optimized and that the overall convergence of RE simulations can be dramatically accelerated.

Authors:

Vogel, Thomas ^[1]; Perez, Danny ^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Publication Date:: Thu Nov 05 00:00:00 EST 2015

Research Org.:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1239374

Alternate Identifier(s):: OSTI ID: 1225240

Report Number(s):: LA-UR-15-23605
Journal ID: ISSN 0031-9007; PRLTAO

Grant/Contract Number:: AC52-06NA25396

Resource Type:: Accepted Manuscript

Journal Name:: Physical Review Letters

Additional Journal Information:: Journal Volume: 115; Journal Issue: 19; Journal ID: ISSN 0031-9007

Publisher:: American Physical Society (APS)

Country of Publication:: United States

Language:: English

Subject:: 99 GENERAL AND MISCELLANEOUS; 97 MATHEMATICS AND COMPUTING

Citation Formats


                    Vogel, Thomas, and Perez, Danny. Towards an optimal flow: Density-of-states-informed replica-exchange simulations.  United States: N. p., 2015. 
Web.  doi:10.1103/PhysRevLett.115.190602.

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                    Vogel, Thomas, & Perez, Danny. Towards an optimal flow: Density-of-states-informed replica-exchange simulations.  United States.  https://doi.org/10.1103/PhysRevLett.115.190602

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                    Vogel, Thomas, and Perez, Danny. Thu .  
"Towards an optimal flow: Density-of-states-informed replica-exchange simulations".  United States.  https://doi.org/10.1103/PhysRevLett.115.190602.  https://www.osti.gov/servlets/purl/1239374.

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@article{osti_1239374,

  title        = {Towards an optimal flow: Density-of-states-informed replica-exchange simulations},

  author       = {Vogel, Thomas and Perez, Danny},

  abstractNote = {Here we learn that replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around phase transitions, or when a few hard-to-find configurations dominate the statistical averages. We introduce a generalized RE scheme, density-of-states-informed RE, that addresses some of these challenges. The key feature of our approach is to inform the simulation with readily available, but commonly unused, information on the density of states of the system as the RE simulation proceeds. This enables two improvements, namely, the introduction of resampling moves that actively move the system towards equilibrium and the continual adaptation of the optimal temperature set. As a consequence of these two innovations, we show that the configuration flow in temperature space is optimized and that the overall convergence of RE simulations can be dramatically accelerated.},

  doi          = {10.1103/PhysRevLett.115.190602},

  journal      = {Physical Review Letters},

  number       = 19,

  volume       = 115,

  place        = {United States},

  year         = {Thu Nov 05 00:00:00 EST 2015},

  month        = {Thu Nov 05 00:00:00 EST 2015}

}

Copy to clipboard

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Works referencing / citing this record:

Approximate ground states of the random-field Potts model from graph cuts
journal, May 2018

Kumar, Manoj; Kumar, Ravinder; Weigel, Martin
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Similar Records

Title: Towards an optimal flow: Density-of-states-informed replica-exchange simulations

Abstract

Citation Formats

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles journal, February 1992

Parallel tempering: Theory, applications, and new perspectives journal, January 2005

Critical behavior of three-dimensional Ising spin glass models journal, December 2008

Evidence of Non-Mean-Field-Like Low-Temperature Behavior in the Edwards-Anderson Spin-Glass Model journal, October 2012

Free-energy barriers in the Sherrington-Kirkpatrick model journal, April 2006

Effects of the interaction range on structural phases of flexible polymers journal, February 2013

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder journal, May 2005

A biased Monte Carlo scheme for zeolite structure solution journal, January 1999

Prediction of absolute crystal-nucleation rate in hard-sphere colloids journal, February 2001

Structure of Si(114) determined by global optimization methods journal, March 2005

Generalized ensemble and tempering simulations: A unified view journal, February 2007

Escaping free-energy minima journal, September 2002

Statistical-Temperature Monte Carlo and Molecular Dynamics Algorithms journal, August 2006

Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang–Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics journal, April 2014

Adaptive biasing force method for scalar and vector free energy calculations journal, April 2008

Dynamical Approach to Temperature journal, February 1997

Configurational temperature: Verification of Monte Carlo simulations journal, October 1998

Some comments on Monte Carlo and molecular dynamics methods journal, December 2013

Microcanonical Analyses of Peptide Aggregation Processes journal, November 2006

Microcanonical entropy inflection points: Key to systematic understanding of transitions in finite systems journal, July 2011

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing journal, November 2011

Optimal allocation of replicas in parallel tempering simulations journal, January 2005

Feedback-optimized parallel tempering Monte Carlo journal, March 2006

Optimized parallel tempering simulations of proteins journal, May 2006

Efficient parallel tempering for first-order phase transitions journal, October 2007

A temperature predictor for parallel tempering simulations journal, January 2008

Make Life Simple: Unleash the Full Power of the Parallel Tempering Algorithm journal, September 2008

Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations journal, November 2014

An embedded-atom potential for the Cu–Ag system journal, May 2006

Comparative study of microstructural evolution during melting and crystallization journal, July 2006

Molecular dynamics simulation for cooling rate dependence of solidification microstructures of silver journal, August 2008

Simulation of molecular dynamics of silver subcritical nuclei and crystal clusters during solidification journal, November 2010

The cooling rate dependence of crystallization for liquid copper: A molecular dynamics study journal, May 2001

Atomistic structural evolution with cooling rates during the solidification of liquid nickel journal, May 2011

Generalized Replica Exchange Method journal, June 2010

Replica Exchange Statistical Temperature Molecular Dynamics Algorithm journal, February 2012

Generic, Hierarchical Framework for Massively Parallel Wang-Landau Sampling journal, May 2013

Scalable replica-exchange framework for Wang-Landau sampling journal, August 2014

Approximate ground states of the random-field Potts model from graph cuts journal, May 2018

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
journal, February 1992

Parallel tempering: Theory, applications, and new perspectives
journal, January 2005

Critical behavior of three-dimensional Ising spin glass models
journal, December 2008

Evidence of Non-Mean-Field-Like Low-Temperature Behavior in the Edwards-Anderson Spin-Glass Model
journal, October 2012

Free-energy barriers in the Sherrington-Kirkpatrick model
journal, April 2006

Effects of the interaction range on structural phases of flexible polymers
journal, February 2013

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
journal, May 2005

A biased Monte Carlo scheme for zeolite structure solution
journal, January 1999

Prediction of absolute crystal-nucleation rate in hard-sphere colloids
journal, February 2001

Structure of Si(114) determined by global optimization methods
journal, March 2005

Generalized ensemble and tempering simulations: A unified view
journal, February 2007

Escaping free-energy minima
journal, September 2002

Statistical-Temperature Monte Carlo and Molecular Dynamics Algorithms
journal, August 2006

Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang–Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics
journal, April 2014

Adaptive biasing force method for scalar and vector free energy calculations
journal, April 2008

Dynamical Approach to Temperature
journal, February 1997

Configurational temperature: Verification of Monte Carlo simulations
journal, October 1998

Some comments on Monte Carlo and molecular dynamics methods
journal, December 2013

Microcanonical Analyses of Peptide Aggregation Processes
journal, November 2006

Microcanonical entropy inflection points: Key to systematic understanding of transitions in finite systems
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Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
journal, November 2011

Optimal allocation of replicas in parallel tempering simulations
journal, January 2005

Feedback-optimized parallel tempering Monte Carlo
journal, March 2006

Optimized parallel tempering simulations of proteins
journal, May 2006

Efficient parallel tempering for first-order phase transitions
journal, October 2007

A temperature predictor for parallel tempering simulations
journal, January 2008

Make Life Simple: Unleash the Full Power of the Parallel Tempering Algorithm
journal, September 2008

Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations
journal, November 2014

An embedded-atom potential for the Cu–Ag system
journal, May 2006

Comparative study of microstructural evolution during melting and crystallization
journal, July 2006

Molecular dynamics simulation for cooling rate dependence of solidification microstructures of silver
journal, August 2008

Simulation of molecular dynamics of silver subcritical nuclei and crystal clusters during solidification
journal, November 2010

The cooling rate dependence of crystallization for liquid copper: A molecular dynamics study
journal, May 2001

Atomistic structural evolution with cooling rates during the solidification of liquid nickel
journal, May 2011

Generalized Replica Exchange Method
journal, June 2010

Replica Exchange Statistical Temperature Molecular Dynamics Algorithm
journal, February 2012

Generic, Hierarchical Framework for Massively Parallel Wang-Landau Sampling
journal, May 2013

Scalable replica-exchange framework for Wang-Landau sampling
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Approximate ground states of the random-field Potts model from graph cuts
journal, May 2018