Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
Abstract
Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.
- Authors:
-
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
- OSTI Identifier:
- 1374573
- Grant/Contract Number:
- AC02-06CH11357; U54-GM087519
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 145; Journal Issue: 13; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; constant pH; expanded ensemble; linear response; nonequilibrium MD/MC
Citation Formats
Radak, Brian K., and Roux, Benoît. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations. United States: N. p., 2016.
Web. doi:10.1063/1.4964288.
Radak, Brian K., & Roux, Benoît. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations. United States. https://doi.org/10.1063/1.4964288
Radak, Brian K., and Roux, Benoît. Fri .
"Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations". United States. https://doi.org/10.1063/1.4964288. https://www.osti.gov/servlets/purl/1374573.
@article{osti_1374573,
title = {Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations},
author = {Radak, Brian K. and Roux, Benoît},
abstractNote = {Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.},
doi = {10.1063/1.4964288},
journal = {Journal of Chemical Physics},
number = 13,
volume = 145,
place = {United States},
year = {Fri Oct 07 00:00:00 EDT 2016},
month = {Fri Oct 07 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods
journal, October 2003
- Shirts, Michael R.; Bair, Eric; Hooker, Giles
- Physical Review Letters, Vol. 91, Issue 14
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
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977
- Torrie, G. M.; Valleau, J. P.
- Journal of Computational Physics, Vol. 23, Issue 2
Molecular simulation with variable protonation states at constant pH
journal, April 2007
- Stern, Harry A.
- The Journal of Chemical Physics, Vol. 126, Issue 16
Thermodynamic Metrics and Optimal Paths
journal, May 2012
- Sivak, David A.; Crooks, Gavin E.
- Physical Review Letters, Vol. 108, Issue 19
Optimum protocol for fast-switching free-energy calculations
journal, February 2010
- Geiger, Philipp; Dellago, Christoph
- Physical Review E, Vol. 81, Issue 2
Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap
journal, May 2012
- Ballard, Andrew J.; Jarzynski, Christopher
- The Journal of Chemical Physics, Vol. 136, Issue 19
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
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
Absolute entropy of simple point charge model water by adiabatic switching processes
journal, August 1994
- Tsao, Li‐Wen; Sheu, Sheh‐Yi; Mou, Chung‐Yuan
- The Journal of Chemical Physics, Vol. 101, Issue 3
Improved convergence in dual-topology free energy calculations through use of harmonic restraints
journal, August 1998
- Axelsen, Paul H.; Li, Daohui
- Journal of Computational Chemistry, Vol. 19, Issue 11
Optimizing the driving function for nonequilibrium free-energy calculations in the linear regime: A variational approach
journal, March 2005
- de Koning, Maurice
- The Journal of Chemical Physics, Vol. 122, Issue 10
Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
journal, September 1999
- Crooks, Gavin E.
- Physical Review E, Vol. 60, Issue 3
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
Optimal Finite-Time Processes In Stochastic Thermodynamics
journal, March 2007
- Schmiedl, Tim; Seifert, Udo
- Physical Review Letters, Vol. 98, Issue 10
Adiabatic switching applied to realistic crystalline solids: Vacancy-formation free energy in copper
journal, January 1997
- de Koning, M.; Antonelli, A.
- Physical Review B, Vol. 55, Issue 2
Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
journal, March 2014
- Sivak, David A.; Chodera, John D.; Crooks, Gavin E.
- The Journal of Physical Chemistry B, Vol. 118, Issue 24
Einstein crystal as a reference system in free energy estimation using adiabatic switching
journal, January 1996
- de Koning, M.; Antonelli, A.
- Physical Review E, Vol. 53, Issue 1
Nonequilibrium Equality for Free Energy Differences
journal, April 1997
- Jarzynski, C.
- Physical Review Letters, Vol. 78, Issue 14
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
journal, October 2003
- Gore, J.; Ritort, F.; Bustamante, C.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics—Monte Carlo simulations
journal, January 2015
- Chen, Yunjie; Roux, Benoît
- The Journal of Chemical Physics, Vol. 142, Issue 2
Simple analysis of noise and hysteresis in (slow-growth) free energy simulations
journal, November 1991
- Hermans, Jan
- The Journal of Physical Chemistry, Vol. 95, Issue 23
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
journal, November 2012
- Vanommeslaeghe, K.; MacKerell, A. D.
- Journal of Chemical Information and Modeling, Vol. 52, Issue 12
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
Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method
journal, July 2015
- Chen, Yunjie; Roux, Benoît
- Journal of Chemical Theory and Computation, Vol. 11, Issue 8
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
journal, November 2012
- Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.
- Journal of Chemical Information and Modeling, Vol. 52, Issue 12
Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems
journal, January 1998
- Crooks, Gavin E.
- Journal of Statistical Physics, Vol. 90, Issue 5/6, p. 1481-1487
The fluctuation-dissipation theorem
journal, January 1966
- Kubo, R.
- Reports on Progress in Physics, Vol. 29, Issue 1
Works referencing / citing this record:
Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator
journal, January 2018
- Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe
- The Journal of Chemical Physics, Vol. 148, Issue 1
A generalized linear response framework for expanded ensemble and replica exchange simulations
journal, August 2018
- Radak, Brian K.; Suh, Donghyuk; Roux, Benoît
- The Journal of Chemical Physics, Vol. 149, Issue 7
Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches
journal, October 2019
- Procacci, Piero
- The Journal of Chemical Physics, Vol. 151, Issue 14
Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates
journal, October 2019
- Procacci, Piero
- The Journal of Chemical Physics, Vol. 151, Issue 14
Scalable molecular dynamics on CPU and GPU architectures with NAMD
journal, July 2020
- Phillips, James C.; Hardy, David J.; Maia, Julio D. C.
- The Journal of Chemical Physics, Vol. 153, Issue 4