An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

Rick, Steven W.; Schwing, Gregory J.; Summa, Christopher M.

doi:10.1021/acs.jcim.0c01236

Title: An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

Journal Article · 26 January 2021 · Journal of Chemical Information and Modeling

DOI:https://doi.org/10.1021/acs.jcim.0c01236· OSTI ID:1851617

^[1]; Schwing, Gregory J. ^[2]; Summa, Christopher M. ^[2]

Univ. of New Orleans, New Orleans, LA (United States). Dept. of Chemistry
Univ. of New Orleans, New Orleans, LA (United States). Dept. of Computer Science

An implementation of the replica exchange with dynamical scaling (REDS) method in the commonly used molecular dynamics program GROMACS is presented. REDS is a replica exchange method that requires fewer replicas than conventional replica exchange while still providing data over a range of temperatures and can be used in either constant volume or constant pressure ensembles. Details for running REDS simulations are given, and an application to the human islet amyloid polypeptide (hIAPP) 11-25 fragment shows that the model efficiently samples conformational space.

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Research Organization:: Louisiana State Univ., Baton Rouge, LA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0012432

OSTI ID:: 1851617

Journal Information:: Journal of Chemical Information and Modeling, Vol. 61, Issue 2; ISSN 1549-9596

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (91)

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction Fukunishi, Hiroaki; Watanabe, Osamu; Takada, Shoji The Journal of Chemical Physics, Vol. 116, Issue 20 https://doi.org/10.1063/1.1472510	journal	May 2002
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling Torrie, G. M.; Valleau, J. P. Journal of Computational Physics, Vol. 23, Issue 2 https://doi.org/10.1016/0021-9991(77)90121-8	journal	February 1977
Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities Gallicchio, Emilio; Lapelosa, Mauro; Levy, Ronald M. Journal of Chemical Theory and Computation, Vol. 6, Issue 9 https://doi.org/10.1021/ct1002913	journal	August 2010
Replica exchange with solute tempering: A method for sampling biological systems in explicit water Liu, P.; Kim, B.; Friesner, R. A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 39 https://doi.org/10.1073/pnas.0506346102	journal	September 2005
Atomistic Monte Carlo simulation of cis -1,4 polyisoprene melts. II. Parallel tempering end-bridging Monte Carlo simulations Doxastakis, M.; Mavrantzas, V. G.; Theodorou, D. N. The Journal of Chemical Physics, Vol. 115, Issue 24 https://doi.org/10.1063/1.1416491	journal	December 2001
Simulating replica exchange simulations of protein folding with a kinetic network model Zheng, W.; Andrec, M.; Gallicchio, E. Proceedings of the National Academy of Sciences, Vol. 104, Issue 39 https://doi.org/10.1073/pnas.0704418104	journal	September 2007
Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets Vogel, Thomas; Perez, Danny Physics Procedia, Vol. 68 https://doi.org/10.1016/j.phpro.2015.07.121	journal	January 2015
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides ^† Kaminski, George A.; Friesner, Richard A.; Tirado-Rives, Julian The Journal of Physical Chemistry B, Vol. 105, Issue 28 https://doi.org/10.1021/jp003919d	journal	July 2001
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Exchange Monte Carlo Method and Application to Spin Glass Simulations Hukushima, Koji; Nemoto, Koji Journal of the Physical Society of Japan, Vol. 65, Issue 6 https://doi.org/10.1143/JPSJ.65.1604	journal	June 1996
Resolution Exchange Simulation Lyman, Edward; Ytreberg, F. Marty; Zuckerman, Daniel M. Physical Review Letters, Vol. 96, Issue 2 https://doi.org/10.1103/PhysRevLett.96.028105	journal	January 2006
Replica Exchange Statistical Temperature Molecular Dynamics Algorithm Kim, Jaegil; Straub, John E.; Keyes, Tom The Journal of Physical Chemistry B, Vol. 116, Issue 29 https://doi.org/10.1021/jp300366j	journal	February 2012
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo Chemical Science, Vol. 9, Issue 4 https://doi.org/10.1039/C7SC04531J	journal	January 2018
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent Liu, Pu; Huang, Xuhui; Zhou, Ruhong The Journal of Physical Chemistry B, Vol. 110, Issue 38 https://doi.org/10.1021/jp060365r	journal	July 2006
Modified Replica Exchange Simulation Methods for Local Structure Refinement Cheng, Xiaolin; Cui, Guanglei; Hornak, Viktor The Journal of Physical Chemistry B, Vol. 109, Issue 16 https://doi.org/10.1021/jp045437y	journal	April 2005
Replica-Exchange Method Using the Generalized Effective Potential Jang, Soonmin; Shin, Seokmin; Pak, Youngshang Physical Review Letters, Vol. 91, Issue 5 https://doi.org/10.1103/PhysRevLett.91.058305	journal	August 2003
Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2) Wang, Lingle; Friesner, Richard A.; Berne, B. J. The Journal of Physical Chemistry B, Vol. 115, Issue 30 https://doi.org/10.1021/jp204407d	journal	August 2011
Cool walking: A new Markov chain Monte Carlo sampling method Brown, Scott; Head-Gordon, Teresa Journal of Computational Chemistry, Vol. 24, Issue 1 https://doi.org/10.1002/jcc.10181	journal	December 2002
How hot? Systematic convergence of the replica exchange method using multiple reservoirs Ruscio, Jory Z.; Fawzi, Nicolas L.; Head-Gordon, Teresa Journal of Computational Chemistry https://doi.org/10.1002/jcc.21355	journal	January 2009
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
GROMACS: A message-passing parallel molecular dynamics implementation Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00042-E	journal	September 1995
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V. The Journal of Chemical Physics, Vol. 96, Issue 3 https://doi.org/10.1063/1.462133	journal	February 1992
Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths ^† Gallicchio, Emilio; Andrec, Michael; Felts, Anthony K. The Journal of Physical Chemistry B, Vol. 109, Issue 14 https://doi.org/10.1021/jp045294f	journal	April 2005
Improving replica exchange using driven scaling Lee, Alexis J.; Rick, Steven W. The Journal of Chemical Physics, Vol. 131, Issue 17 https://doi.org/10.1063/1.3259049	journal	November 2009
Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes Liu, Pu; Voth, Gregory A. The Journal of Chemical Physics, Vol. 126, Issue 4 https://doi.org/10.1063/1.2408415	journal	January 2007
Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example Qi, Ruxi; Wei, Guanghong; Ma, Buyong Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-7811-3_5	book	January 2018
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Kabsch, Wolfgang; Sander, Christian Biopolymers, Vol. 22, Issue 12 https://doi.org/10.1002/bip.360221211	journal	December 1983
Optimized Monte Carlo data analysis Ferrenberg, Alan M.; Swendsen, Robert H. Physical Review Letters, Vol. 63, Issue 12 https://doi.org/10.1103/PhysRevLett.63.1195	journal	September 1989
Generalized parallel sampling Whitfield, T. W.; Bu, L.; Straub, J. E. Physica A: Statistical Mechanics and its Applications, Vol. 305, Issue 1-2 https://doi.org/10.1016/S0378-4371(01)00656-2	journal	March 2002
Determination of liquid–solid transition using histogram reweighting method and expanded ensemble simulations Chang, Jaeeon; Sandler, Stanley I. The Journal of Chemical Physics, Vol. 118, Issue 18 https://doi.org/10.1063/1.1565329	journal	May 2003
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong PLOS Computational Biology, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pcbi.1004619	journal	April 2016
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
A temperature predictor for parallel tempering simulations Patriksson, Alexandra; van der Spoel, David Physical Chemistry Chemical Physics, Vol. 10, Issue 15 https://doi.org/10.1039/b716554d	journal	January 2008
Statistically optimal analysis of samples from multiple equilibrium states Shirts, Michael R.; Chodera, John D. The Journal of Chemical Physics, Vol. 129, Issue 12 https://doi.org/10.1063/1.2978177	journal	September 2008
Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ ₄₂ peptide Han, Ming; Hansmann, Ulrich H. E. The Journal of Chemical Physics, Vol. 135, Issue 6 https://doi.org/10.1063/1.3617250	journal	August 2011
Replica exchange with dynamical scaling Rick, Steven W. The Journal of Chemical Physics, Vol. 126, Issue 5 https://doi.org/10.1063/1.2431807	journal	February 2007
Negative activation enthalpies in the kinetics of protein folding. Oliveberg, M.; Tan, Y. J.; Fersht, A. R. Proceedings of the National Academy of Sciences, Vol. 92, Issue 19 https://doi.org/10.1073/pnas.92.19.8926	journal	September 1995
Conformational Distribution and α-Helix to β-Sheet Transition of Human Amylin Fragment Dimer Qi, Ruxi; Luo, Yin; Ma, Buyong Biomacromolecules, Vol. 15, Issue 1 https://doi.org/10.1021/bm401406e	journal	December 2013
TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent Li, Xianfeng; Snyder, James A.; Stuart, Steven J. The Journal of Chemical Physics, Vol. 143, Issue 14 https://doi.org/10.1063/1.4932341	journal	October 2015
Replica exchange with nonequilibrium switches Ballard, A. J.; Jarzynski, C. Proceedings of the National Academy of Sciences, Vol. 106, Issue 30 https://doi.org/10.1073/pnas.0900406106	journal	July 2009
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Mayor, U.; Johnson, C. M.; Daggett, V. Proceedings of the National Academy of Sciences, Vol. 97, Issue 25 https://doi.org/10.1073/pnas.250473497	journal	November 2000
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential Kannan, Srinivasaraghavan; Zacharias, Martin Proteins: Structure, Function, and Bioinformatics, Vol. 66, Issue 3 https://doi.org/10.1002/prot.21258	journal	November 2006
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software Zuckerman, Daniel M.; Chong, Lillian T. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-070816-033834	journal	May 2017
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations Chodera, John D.; Swope, William C.; Pitera, Jed W. Journal of Chemical Theory and Computation, Vol. 3, Issue 1 https://doi.org/10.1021/ct0502864	journal	November 2006
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics Eastman, Peter; Swails, Jason; Chodera, John D. PLOS Computational Biology, Vol. 13, Issue 7 https://doi.org/10.1371/journal.pcbi.1005659	journal	July 2017
Replica-exchange simulated tempering method for simulations of frustrated systems Mitsutake, Ayori; Okamoto, Yuko Chemical Physics Letters, Vol. 332, Issue 1-2 https://doi.org/10.1016/S0009-2614(00)01262-8	journal	December 2000
Smart Darting Monte Carlo Andricioaei, Ioan; Straub, John E.; Voter, Arthur F. The Journal of Chemical Physics, Vol. 114, Issue 16 https://doi.org/10.1063/1.1358861	journal	April 2001
Enhanced sampling techniques in molecular dynamics simulations of biological systems Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850, Issue 5 https://doi.org/10.1016/j.bbagen.2014.10.019	journal	May 2015
Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations Daura, Xavier; van Gunsteren, Wilfred F.; Mark, Alan E. Proteins: Structure, Function, and Genetics, Vol. 34, Issue 3 https://doi.org/10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO;2-3	journal	February 1999
On the Infinite Swapping Limit for Parallel Tempering Dupuis, Paul; Liu, Yufei; Plattner, Nuria Multiscale Modeling & Simulation, Vol. 10, Issue 3 https://doi.org/10.1137/110853145	journal	January 2012
Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations Hicks, Alan; Zhou, Huan-Xiang The Journal of Chemical Physics, Vol. 149, Issue 7 https://doi.org/10.1063/1.5027409	journal	August 2018
A statistical analysis of the precision of reweighting-based simulations Shen, Tongye; Hamelberg, Donald The Journal of Chemical Physics, Vol. 129, Issue 3 https://doi.org/10.1063/1.2944250	journal	July 2008
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration Abrams, Cameron; Bussi, Giovanni Entropy, Vol. 16, Issue 1 https://doi.org/10.3390/e16010163	journal	December 2013
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Equilibrium Sampling in Biomolecular Simulations Zuckerman, Daniel M. Annual Review of Biophysics, Vol. 40, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155255	journal	June 2011
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent Periole, Xavier; Mark, Alan E. The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2404954	journal	January 2007
Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations Abraham, Mark J.; Gready, Jill E. Journal of Chemical Theory and Computation, Vol. 4, Issue 7 https://doi.org/10.1021/ct800016r	journal	May 2008
Multicanonical parallel tempering Faller, Roland; Yan, Qiliang; de Pablo, Juan J. The Journal of Chemical Physics, Vol. 116, Issue 13 https://doi.org/10.1063/1.1456504	journal	April 2002
GROMACS 3.0: a package for molecular simulation and trajectory analysis Lindahl, Erik; Hess, Berk; van der Spoel, David Journal of Molecular Modeling, Vol. 7, Issue 8 https://doi.org/10.1007/s008940100045	journal	August 2001
Increasing the Efficiency of Free Energy Calculations Using Parallel Tempering and Histogram Reweighting Rick, Steven W. Journal of Chemical Theory and Computation, Vol. 2, Issue 4 https://doi.org/10.1021/ct050207o	journal	May 2006
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Exchange Often and Properly in Replica Exchange Molecular Dynamics Sindhikara, Daniel J.; Emerson, Daniel J.; Roitberg, Adrian E. Journal of Chemical Theory and Computation, Vol. 6, Issue 9 https://doi.org/10.1021/ct100281c	journal	July 2010
Two-dimensional replica-exchange method for predicting protein-ligand binding structures Kokubo, Hironori; Tanaka, Toshimasa; Okamoto, Yuko Journal of Computational Chemistry, Vol. 34, Issue 30 https://doi.org/10.1002/jcc.23427	journal	September 2013
Replica-exchange molecular dynamics simulation for supercooled liquids Yamamoto, Ryoichi; Kob, Walter Physical Review E, Vol. 61, Issue 5 https://doi.org/10.1103/PhysRevE.61.5473	journal	May 2000
Microcanonical replica exchange molecular dynamics simulation of proteins Kar, Parimal; Nadler, Walter; Hansmann, Ulrich H. E. Physical Review E, Vol. 80, Issue 5 https://doi.org/10.1103/PhysRevE.80.056703	journal	November 2009
An improved replica-exchange sampling method: Temperature intervals with global energy reassignment Li, Xianfeng; O’Brien, Christopher P.; Collier, Galen The Journal of Chemical Physics, Vol. 127, Issue 16 https://doi.org/10.1063/1.2780152	journal	October 2007
How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach Nymeyer, Hugh Journal of Chemical Theory and Computation, Vol. 4, Issue 4 https://doi.org/10.1021/ct7003337	journal	February 2008
Energy component analysis for dilute aqueous solutions of lithium(1+), sodium(1+), fluoride(1-), and chloride(1-) ions Chandrasekhar, Jayaraman; Spellmeyer, David C.; Jorgensen, William L. Journal of the American Chemical Society, Vol. 106, Issue 4 https://doi.org/10.1021/ja00316a012	journal	February 1984
The combined force field-sampling problem in simulations of disordered amyloid-β peptides Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa The Journal of Chemical Physics, Vol. 150, Issue 10 https://doi.org/10.1063/1.5078615	journal	March 2019
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2 https://doi.org/10.1002/wcms.1121	journal	September 2012
Error and efficiency of replica exchange molecular dynamics simulations Rosta, Edina; Hummer, Gerhard The Journal of Chemical Physics, Vol. 131, Issue 16 https://doi.org/10.1063/1.3249608	journal	October 2009
LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules Hamelberg, Donald; Mongan, John; McCammon, J. Andrew The Journal of Chemical Physics, Vol. 120, Issue 24 https://doi.org/10.1063/1.1755656	journal	June 2004
Expanded ensemble and replica exchange methods for simulation of protein-like systems Fenwick, Michael K.; Escobedo, Fernando A. The Journal of Chemical Physics, Vol. 119, Issue 22 https://doi.org/10.1063/1.1624822	journal	December 2003
Umbrella sampling: Umbrella sampling Kästner, Johannes Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6 https://doi.org/10.1002/wcms.66	journal	May 2011
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal Journal of Computational Chemistry, Vol. 13, Issue 8 https://doi.org/10.1002/jcc.540130812	journal	October 1992
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations Kutzner, Carsten; Páll, Szilárd; Fechner, Martin Journal of Computational Chemistry, Vol. 36, Issue 26 https://doi.org/10.1002/jcc.24030	journal	August 2015
Does Replica Exchange with Solute Tempering Efficiently Sample Aβ Peptide Conformational Ensembles? Smith, Amy K.; Lockhart, Christopher; Klimov, Dmitri K. Journal of Chemical Theory and Computation, Vol. 12, Issue 10 https://doi.org/10.1021/acs.jctc.6b00660	journal	September 2016
Rate−Temperature Relationships in λ-Repressor Fragment λ ₆ _- ₈₅ Folding Yang, Wei Yuan; Gruebele, Martin Biochemistry, Vol. 43, Issue 41 https://doi.org/10.1021/bi049113b	journal	September 2004
Weighted-ensemble Brownian dynamics simulations for protein association reactions Huber, G. A.; Kim, S. Biophysical Journal, Vol. 70, Issue 1 https://doi.org/10.1016/S0006-3495(96)79552-8	journal	January 1996
Exchange frequency in replica exchange molecular dynamics Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E. The Journal of Chemical Physics, Vol. 128, Issue 2 https://doi.org/10.1063/1.2816560	journal	January 2008
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models Miyamoto, Shuichi; Kollman, Peter A. Journal of Computational Chemistry, Vol. 13, Issue 8 https://doi.org/10.1002/jcc.540130805	journal	October 1992
Simulated Tempering: A New Monte Carlo Scheme Marinari, E.; Parisi, G. Europhysics Letters (EPL), Vol. 19, Issue 6 https://doi.org/10.1209/0295-5075/19/6/002	journal	July 1992
Entropic tempering: A method for overcoming quasiergodicity in simulation Calvo, F.; Doye, J. P. K. Physical Review E, Vol. 63, Issue 1 https://doi.org/10.1103/PhysRevE.63.010902	journal	December 2000
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Escaping free-energy minima Laio, A.; Parrinello, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.202427399	journal	September 2002
On the Efficiency of Exchange in Parallel Tempering Monte Carlo Simulations Predescu, Cristian; Predescu, Mihaela; Ciobanu, Cristian V. The Journal of Physical Chemistry B, Vol. 109, Issue 9 https://doi.org/10.1021/jp045073+	journal	February 2005
On performance measures for infinite swapping Monte Carlo methods Doll, J. D.; Dupuis, Paul The Journal of Chemical Physics, Vol. 142, Issue 2 https://doi.org/10.1063/1.4904890	journal	January 2015
Replica-exchange extensions of simulated tempering method Mitsutake, Ayori; Okamoto, Yuko The Journal of Chemical Physics, Vol. 121, Issue 6 https://doi.org/10.1063/1.1766015	journal	January 2004

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Title: An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

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