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We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions.
Comparison of simple potential functions for simulating liquid water
William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, and Michael L. Klein · 1983
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H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma · 1987
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Molecullar dynamics algorithm for multiple time scales: Systems with disparate masses
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Gibson D.A. and E.A. Carter · 1993
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Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, and Lee G. Pedersen · 1995
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Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
K. Anton Feenstra, Berk Hess, and Herman J. C. Berendsen · 1999
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How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules?
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Efficient multiple time step method for use with ewald and particle mesh ewald for large biomolecular systems
Ruhong Zhou, Edward Harder, Huafeng Xu, and B. J. Berne · 2001
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Verlet-i/r-respa/impulse is limited by nonlinear instabilities
Q. Ma, J. Izaguirre, and R. Skeel · 2003
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Scalable molecular dynamics with namd
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Canonical sampling through velocity rescaling
Giovanni Bussi, Davide Donadio, and Michele Parrinello · 2007
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Millisecond-scale molecular dynamics simulations on anton
David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles · 2009
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Molecular dynamics with multiple time scales: How to avoid pitfalls
Joseph A. Morrone, Ruhong Zhou, and B. J. Berne · 2010
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Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances
Joseph A. Morrone, Thomas E. Markland, Michele Ceriotti, and B. J. Berne · 2011
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Rational Construction of Stochastic Numerical Methods for Molecular Sampling
Charles Matthews and Benedict Leimkuhler · 2012
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Rejection-free monte carlo sampling for general potentials
E. A. J. F. Peters and G. de With · 2012
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An overview of the amber biomolecular simulation package
Romelia Salomon-Ferrer, David A. Case, and Ross C. Walker · 2013
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Robust and efficient configurational molecular sampling via langevin dynamics
Genesis 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, and Yuji Sugita · 2017
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Piecewise Deterministic Markov Chain Monte Carlo
P. Vanetti, A. Bouchard-Côté, G. Deligiannidis, and A. Doucet · 2017
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L. de Groot, Helmut Grubmueller, and Alexander D. MacKerell, Jr · 2017
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Tinker-hp: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Fèlix Aviat, Benjamin Stamm, Zhifeng F. Jing, Matthew Harger, Hedieh Torabifard, G. Andrès Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday, Pengyu Y. Ren, Jay W. Ponder, and Jean-Philip Piquemal · 2018
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Benedict Leimkuhler and Charles Matthews · 2013
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Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
Ben Leimkuhler, Daniel T. Margul, and Mark E. Tuckerman · 2013
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Rational construction of stochastic numerical methods for molecular sampling
B. Leimkuhler and C. Matthews · 2013
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New faster charmm molecular dynamics engine
Antti-Pekka Hynninen and Michael F. Crowley · 2014
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Time integrators for molecular dynamics
N. Bou-Rabee · 2014
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Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilard Pall, Jeremy C. Smith, Berk Hess, and Erik Lindahl · 2015
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Polarizable Force Fields for Biomolecular Modeling
Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip Piquemal · 2015
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A. Durmus, A. Guillin, and P. Monmarché · 2018
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Geometric ergodicity of the bouncy particle sampler
A. Durmus, A. Guillin, and P. Monmarché · 2018
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P. Monmarché · 2018
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Combining iteration-free polarization with large time step stochastic-isokinetic integration
Alex Albaugh, Mark E. Tuckerman, and Teresa Head-Gordon · 2019
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Pushing the limits of multiple-time-step strategies for polarizable point dipole molecular dynamics
Louis Lagardère, Félix Aviat, and Jean-Philip Piquemal · 2019
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Raising the performance of the tinker-hp molecular modeling package [article v1.0]
Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Ren, and Jean-Philip Piquemal · 2019
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Accurate biomolecular simulations account for electronic polarization
Josef Melcr and Jean-Philip Piquemal · 2019
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Polarizable force fields for biomolecular simulations: Recent advances and applications
Zhifeng Jing, Chengwen Liu, Sara Y. Cheng, Rui Qi, Brandon D. Walker, Jean-Philip Piquemal, and Pengyu Ren · 2019
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Kinetic walks for sampling
P. Monmarché · 2020
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https://github.com/TinkerTools/Tinker-HP
Tinker-HP’s github · 2020
Closest in time.
http://tinker-hp.ip2ct.upmc.fr/
Tinker-HP’s website · 2020
Closest in time.