skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator

Abstract

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a “boosting phase,” via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolismore » criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [4]
  1. Univ. of Chicago, IL (United States)
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Leadership Computing Facility
  3. Univ. de Lorraine (France); Univ. of Illinois at Urbana-Champaign, IL (United States)
  4. Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1490226
Alternate Identifier(s):
OSTI ID: 1415336
Grant/Contract Number:  
AC02-06CH11357; MCB-1517221
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 148; Journal Issue: 1; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Potential energy surfaces; Monte Carlo methods; Probability theory; Oscillators; Molecular dynamics; Amino acid; Peptides; Free energy; Dielectric properties; Langevin dynamics

Citation Formats

Suh, Donghyuk, Radak, Brian K., Chipot, Christophe, and Roux, Benoît. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator. United States: N. p., 2018. Web. doi:10.1063/1.5004154.
Suh, Donghyuk, Radak, Brian K., Chipot, Christophe, & Roux, Benoît. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator. United States. doi:10.1063/1.5004154.
Suh, Donghyuk, Radak, Brian K., Chipot, Christophe, and Roux, Benoît. Tue . "Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator". United States. doi:10.1063/1.5004154. https://www.osti.gov/servlets/purl/1490226.
@article{osti_1490226,
title = {Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator},
author = {Suh, Donghyuk and Radak, Brian K. and Chipot, Christophe and Roux, Benoît},
abstractNote = {Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a “boosting phase,” via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.},
doi = {10.1063/1.5004154},
journal = {Journal of Chemical Physics},
number = 1,
volume = 148,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
journal, August 2014

  • Comer, Jeffrey; Gumbart, James C.; Hénin, Jérôme
  • The Journal of Physical Chemistry B, Vol. 119, Issue 3
  • DOI: 10.1021/jp506633n

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
journal, November 2014

  • Comer, Jeffrey; Phillips, James C.; Schulten, Klaus
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 12
  • DOI: 10.1021/ct500874p

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
journal, December 2012

  • Arrar, Mehrnoosh; de Oliveira, Cesar Augusto F.; Fajer, Mikolai
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300896h

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal
journal, September 2014

  • Chen, Yunjie; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 141, Issue 11
  • DOI: 10.1063/1.4895516

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
journal, August 2011

  • Wang, Lingle; Friesner, Richard A.; Berne, B. J.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 30
  • DOI: 10.1021/jp204407d

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977


On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
journal, January 2007

  • Christen, Markus; van Gunsteren, Wilfred F.
  • Journal of Computational Chemistry, Vol. 29, Issue 2
  • DOI: 10.1002/jcc.20725

Molecular simulation with variable protonation states at constant pH
journal, April 2007

  • Stern, Harry A.
  • The Journal of Chemical Physics, Vol. 126, Issue 16
  • DOI: 10.1063/1.2731781

Erratum: “Molecular simulation with variable protonation states at constant pH” [J. Chem. Phys. 126, 164112 (2007)]
journal, August 2007

  • Stern, Harry A.
  • The Journal of Chemical Physics, Vol. 127, Issue 7
  • DOI: 10.1063/1.2768942

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
journal, October 2012

  • Jiang, Wei; Luo, Yun; Maragliano, Luca
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 11
  • DOI: 10.1021/ct300468g

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
journal, June 2004

  • Hamelberg, Donald; Mongan, John; McCammon, J. Andrew
  • The Journal of Chemical Physics, Vol. 120, Issue 24
  • DOI: 10.1063/1.1755656

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
journal, July 2010

  • Jiang, Wei; Roux, Benoît
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 9
  • DOI: 10.1021/ct1001768

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model
journal, July 2015

  • Chen, Yunjie; Roux, Benoît
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 8
  • DOI: 10.1021/acs.jctc.5b00372

Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study
journal, November 2008


Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

Improved sampling methods for molecular simulation
journal, April 2007


Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
journal, September 2008

  • Fajer, Mikolai; Hamelberg, Donald; McCammon, J. Andrew
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 10
  • DOI: 10.1021/ct800250m

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

  • Nilmeier, J. P.; Crooks, G. E.; Minh, D. D. L.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 45
  • DOI: 10.1073/pnas.1106094108

Targeting biomolecular flexibility with metadynamics
journal, April 2010

  • Leone, Vanessa; Marinelli, Fabrizio; Carloni, Paolo
  • Current Opinion in Structural Biology, Vol. 20, Issue 2
  • DOI: 10.1016/j.sbi.2010.01.011

Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
journal, March 2010

  • Minoukadeh, K.; Chipot, C.; Lelièvre, T.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 4
  • DOI: 10.1021/ct900524t

Molecular dynamics simulations of biomolecules
journal, September 2002

  • Karplus, Martin; McCammon, J. Andrew
  • Nature Structural Biology, Vol. 9, Issue 9
  • DOI: 10.1038/nsb0902-646

A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
journal, July 2006


All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation
journal, April 2011

  • Wu, Xiongwu; Brooks, Bernard R.
  • The Journal of Chemical Physics, Vol. 134, Issue 13
  • DOI: 10.1063/1.3574397

Self-guided Langevin dynamics via generalized Langevin equation
journal, July 2015

  • Wu, Xiongwu; Brooks, Bernard R.; Vanden-Eijnden, Eric
  • Journal of Computational Chemistry, Vol. 37, Issue 6
  • DOI: 10.1002/jcc.24015

Replica exchange with nonequilibrium switches
journal, July 2009

  • Ballard, A. J.; Jarzynski, C.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 30
  • DOI: 10.1073/pnas.0900406106

Self-guided Langevin dynamics simulation method
journal, November 2003


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

  • Metropolis, Nicholas; Rosenbluth, Arianna W.; Rosenbluth, Marshall N.
  • The Journal of Chemical Physics, Vol. 21, Issue 6
  • DOI: 10.1063/1.1699114

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

  • Park, Sanghyun; Khalili-Araghi, Fatemeh; Tajkhorshid, Emad
  • The Journal of Chemical Physics, Vol. 119, Issue 6
  • DOI: 10.1063/1.1590311

Monte Carlo Sampling Methods Using Markov Chains and Their Applications
journal, April 1970


Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
journal, October 2016

  • Radak, Brian K.; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 145, Issue 13
  • DOI: 10.1063/1.4964288

Enhanced sampling techniques in molecular dynamics simulations of biological systems
journal, May 2015

  • Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
  • Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850, Issue 5
  • DOI: 10.1016/j.bbagen.2014.10.019