The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations

Arad, Evyatar; Farago, Oded; Grønbech‐Jensen, Niels

doi:10.1002/ijch.201500067

Title: The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations

Abstract

Abstract We implement the statistically sound G‐JF thermostat for Langevin dynamics simulations into the ESPResSo molecular package for large‐scale simulations of soft‐matter systems. The implemented integration method is tested against the integrator currently used by the molecular package in simulations of a fluid bilayer membrane. While the latter exhibits deviations in the sampling statistics that increase with the integration time step dt , the former reproduces near‐correct configurational statistics for all dt within the stability range of the simulations. We conclude that, with very modest revisions to existing codes, one can significantly improve the performance of statistical sampling using Langevin thermostats.

Authors:

Arad, Evyatar ^[1]; Farago, Oded ^[2]; Grønbech‐Jensen, Niels ^[3]

Department of Biomedical Engineering Ben Gurion University of the Negev Be'er Sheva 84105 Israel
Department of Biomedical Engineering Ben Gurion University of the Negev Be'er Sheva 84105 Israel, Ilse Katz Institute for Nanoscale Science and Technology Ben Gurion University of the Negev Be'er Sheva 84105 Israel
Department of Mechanical and Aerospace Engineering University of California Davis CA 95616 USA, Department of Mathematics University of California Davis CA 95616 USA

Publication Date:: Thu Apr 07 00:00:00 EDT 2016

Sponsoring Org.:: USDOE

OSTI Identifier:: 1400747

Grant/Contract Number:: NE0000536 000

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Israel Journal of Chemistry

Additional Journal Information:: Journal Name: Israel Journal of Chemistry Journal Volume: 56 Journal Issue: 8; Journal ID: ISSN 0021-2148

Publisher:: Wiley Blackwell (John Wiley & Sons)

Country of Publication:: Israel

Language:: English

Citation Formats


                    Arad, Evyatar, Farago, Oded, and Grønbech‐Jensen, Niels. The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations.  Israel: N. p., 2016. 
Web.  doi:10.1002/ijch.201500067.

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                    Arad, Evyatar, Farago, Oded, & Grønbech‐Jensen, Niels. The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations.  Israel.  https://doi.org/10.1002/ijch.201500067

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                    Arad, Evyatar, Farago, Oded, and Grønbech‐Jensen, Niels. Thu .  
"The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations".  Israel.  https://doi.org/10.1002/ijch.201500067.

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@article{osti_1400747,

  title        = {The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations},

  author       = {Arad, Evyatar and Farago, Oded and Grønbech‐Jensen, Niels},

  abstractNote = {Abstract We implement the statistically sound G‐JF thermostat for Langevin dynamics simulations into the ESPResSo molecular package for large‐scale simulations of soft‐matter systems. The implemented integration method is tested against the integrator currently used by the molecular package in simulations of a fluid bilayer membrane. While the latter exhibits deviations in the sampling statistics that increase with the integration time step dt , the former reproduces near‐correct configurational statistics for all dt within the stability range of the simulations. We conclude that, with very modest revisions to existing codes, one can significantly improve the performance of statistical sampling using Langevin thermostats.},

  doi          = {10.1002/ijch.201500067},

  journal      = {Israel Journal of Chemistry},

  number       = 8,

  volume       = 56,

  place        = {Israel},

  year         = {Thu Apr 07 00:00:00 EDT 2016},

  month        = {Thu Apr 07 00:00:00 EDT 2016}

}

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Works referenced in this record:

Constant pressure and temperature discrete-time Langevin molecular dynamics
journal, November 2014

Grønbech-Jensen, Niels; Farago, Oded
The Journal of Chemical Physics, Vol. 141, Issue 19
DOI: 10.1063/1.4901303

Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions
journal, February 1978

Schneider, T.; Stoll, E.
Physical Review B, Vol. 17, Issue 3
DOI: 10.1103/PhysRevB.17.1302

Canonical dynamics: Equilibrium phase-space distributions
journal, March 1985

Hoover, William G.
Physical Review A, Vol. 31, Issue 3
DOI: 10.1103/PhysRevA.31.1695

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
journal, July 1967

Verlet, Loup
Physical Review, Vol. 159, Issue 1
DOI: 10.1103/PhysRev.159.98

The Art of Molecular Dynamics Simulation
book, January 2004

Rapaport, D. C.
DOI: 10.1017/CBO9780511816581

Equipartition and the Calculation of Temperature in Biomolecular Simulations
journal, May 2010

Eastwood, Michael P.; Stafford, Kate A.; Lippert, Ross A.
Journal of Chemical Theory and Computation, Vol. 6, Issue 7
DOI: 10.1021/ct9002916

A simple and effective Verlet-type algorithm for simulating Langevin dynamics
journal, January 2013

Grønbech-Jensen, Niels; Farago, Oded
Molecular Physics, Vol. 111, Issue 8
DOI: 10.1080/00268976.2012.760055

Temperature in the classical microcanonical ensemble
journal, March 2001

Rickayzen, Gerald; Powles, Jack G.
The Journal of Chemical Physics, Vol. 114, Issue 9
DOI: 10.1063/1.1348024

Tunable generic model for fluid bilayer membranes
journal, July 2005

Cooke, Ira R.; Kremer, Kurt; Deserno, Markus
Physical Review E, Vol. 72, Issue 1
DOI: 10.1103/PhysRevE.72.011506

A unified formulation of the constant temperature molecular dynamics methods
journal, July 1984

Nosé, Shuichi
The Journal of Chemical Physics, Vol. 81, Issue 1
DOI: 10.1063/1.447334

Classical and Quantum Mechanical Hypervirial Theorems
journal, November 1960

Hirschfelder, Joseph O.
The Journal of Chemical Physics, Vol. 33, Issue 5
DOI: 10.1063/1.1731427

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Plimpton, Steve
Journal of Computational Physics, Vol. 117, Issue 1
DOI: 10.1006/jcph.1995.1039

Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
journal, February 2014

Grønbech-Jensen, Niels; Hayre, Natha Robert; Farago, Oded
Computer Physics Communications, Vol. 185, Issue 2
DOI: 10.1016/j.cpc.2013.10.006

Stochastic boundary conditions for molecular dynamics simulations of ST2 water
journal, March 1984

Brünger, Axel; Brooks, Charles L.; Karplus, Martin
Chemical Physics Letters, Vol. 105, Issue 5
DOI: 10.1016/0009-2614(84)80098-6

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Title: The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations

Abstract

Citation Formats

Constant pressure and temperature discrete-time Langevin molecular dynamics journal, November 2014

Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions journal, February 1978

Canonical dynamics: Equilibrium phase-space distributions journal, March 1985

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules journal, July 1967

The Art of Molecular Dynamics Simulation book, January 2004

Equipartition and the Calculation of Temperature in Biomolecular Simulations journal, May 2010

A simple and effective Verlet-type algorithm for simulating Langevin dynamics journal, January 2013

Temperature in the classical microcanonical ensemble journal, March 2001

Tunable generic model for fluid bilayer membranes journal, July 2005

A unified formulation of the constant temperature molecular dynamics methods journal, July 1984

Classical and Quantum Mechanical Hypervirial Theorems journal, November 1960

Fast Parallel Algorithms for Short-Range Molecular Dynamics journal, March 1995

Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations journal, February 2014

Stochastic boundary conditions for molecular dynamics simulations of ST2 water journal, March 1984

Constant pressure and temperature discrete-time Langevin molecular dynamics
journal, November 2014

Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions
journal, February 1978

Canonical dynamics: Equilibrium phase-space distributions
journal, March 1985

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
journal, July 1967

The Art of Molecular Dynamics Simulation
book, January 2004

Equipartition and the Calculation of Temperature in Biomolecular Simulations
journal, May 2010

A simple and effective Verlet-type algorithm for simulating Langevin dynamics
journal, January 2013

Temperature in the classical microcanonical ensemble
journal, March 2001

Tunable generic model for fluid bilayer membranes
journal, July 2005

A unified formulation of the constant temperature molecular dynamics methods
journal, July 1984

Classical and Quantum Mechanical Hypervirial Theorems
journal, November 1960

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
journal, February 2014

Stochastic boundary conditions for molecular dynamics simulations of ST2 water
journal, March 1984