Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation

An, Dong; Cheng, Sara Y.; Head-Gordon, Teresa; Lin, Lin; Lu, Jianfeng

doi:10.1016/j.jcp.2021.110338

Title: Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation

Journal Article · 31 July 2021 · Journal of Computational Physics

DOI: https://doi.org/10.1016/j.jcp.2021.110338 · OSTI ID:1781223

An, Dong;

; Head-Gordon, Teresa;

; Lu, Jianfeng

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Sponsoring Organization:: USDOE

OSTI ID:: 1781223

Journal Information:: Journal of Computational Physics, Journal Name: Journal of Computational Physics Journal Issue: C Vol. 438; ISSN 0021-9991

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (35)

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model Lemkul, Justin A.; Roux, Benoît; van der Spoel, David Journal of Computational Chemistry, Vol. 36, Issue 19 https://doi.org/10.1002/jcc.23937	journal	May 2015
From Ballistic to Diffusive Behavior in Periodic Potentials Hairer, M.; Pavliotis, G. A. Journal of Statistical Physics, Vol. 131, Issue 1 https://doi.org/10.1007/s10955-008-9493-3	journal	February 2008
Extended Lagrangian formalism applied to temperature control and electronic polarization effects in molecular dynamics simulations Van Belle, D.; Wodak, S. J. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00051-G	journal	September 1995
Molecular polarizabilities calculated with a modified dipole interaction Thole, B. T. Chemical Physics, Vol. 59, Issue 3 https://doi.org/10.1016/0301-0104(81)85176-2	journal	August 1981
Quantum dynamics via adiabatic ab initio centroid molecular dynamics Marx, Dominik; Tuckerman, Mark E.; Martyna, Glenn J. Computer Physics Communications, Vol. 118, Issue 2-3 https://doi.org/10.1016/S0010-4655(99)00208-8	journal	May 1999
Homogenization of Hamiltonian systems with a strong constraining potential Bornemann, Folkmar A.; Schütte, Christof Physica D: Nonlinear Phenomena, Vol. 102, Issue 1-2 https://doi.org/10.1016/S0167-2789(96)00245-X	journal	March 1997
Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models Tan, Songchen; Leven, Itai; An, Dong Journal of Chemical Theory and Computation, Vol. 16, Issue 10 https://doi.org/10.1021/acs.jctc.0c00514	journal	September 2020
A New Method for Treating Drude Polarization in Classical Molecular Simulation Albaugh, Alex; Head-Gordon, Teresa Journal of Chemical Theory and Computation, Vol. 13, Issue 11 https://doi.org/10.1021/acs.jctc.7b00838	journal	October 2017
Advanced Potential Energy Surfaces for Molecular Simulation Albaugh, Alex; Boateng, Henry A.; Bradshaw, Richard T. The Journal of Physical Chemistry B, Vol. 120, Issue 37 https://doi.org/10.1021/acs.jpcb.6b06414	journal	August 2016
Accurate Classical Polarization Solution with No Self-Consistent Field Iterations Albaugh, Alex; Niklasson, Anders M. N.; Head-Gordon, Teresa The Journal of Physical Chemistry Letters, Vol. 8, Issue 8 https://doi.org/10.1021/acs.jpclett.7b00450	journal	April 2017
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model Laury, Marie L.; Wang, Lee-Ping; Pande, Vijay S. The Journal of Physical Chemistry B, Vol. 119, Issue 29 https://doi.org/10.1021/jp510896n	journal	September 2014
Current Status of the AMOEBA Polarizable Force Field Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu The Journal of Physical Chemistry B, Vol. 114, Issue 8 https://doi.org/10.1021/jp910674d	journal	March 2010
Why some interfaces cannot be sharp Nakagawa, Naoyuki; Hwang, Harold Y.; Muller, David A. Nature Materials, Vol. 5, Issue 3, p. 204-209 https://doi.org/10.1038/nmat1569	journal	January 2006
Exponential Operators and Parameter Differentiation in Quantum Physics Wilcox, R. M. Journal of Mathematical Physics, Vol. 8, Issue 4 https://doi.org/10.1063/1.1705306	journal	April 1967
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation Niklasson, Anders M. N.; Steneteg, Peter; Odell, Anders The Journal of Chemical Physics, Vol. 130, Issue 21 https://doi.org/10.1063/1.3148075	journal	June 2009
A unified formulation of the constant temperature molecular dynamics methods Nosé, Shuichi The Journal of Chemical Physics, Vol. 81, Issue 1 https://doi.org/10.1063/1.447334	journal	July 1984
Reversible multiple time scale molecular dynamics Tuckerman, M.; Berne, B. J.; Martyna, G. J. The Journal of Chemical Physics, Vol. 97, Issue 3 https://doi.org/10.1063/1.463137	journal	August 1992
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction Albaugh, Alex; Demerdash, Omar; Head-Gordon, Teresa The Journal of Chemical Physics, Vol. 143, Issue 17 https://doi.org/10.1063/1.4933375	journal	November 2015
Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex The Journal of Chemical Physics, Vol. 146, Issue 12 https://doi.org/10.1063/1.4978684	journal	March 2017
Polarity of oxide surfaces and nanostructures Goniakowski, Jacek; Finocchi, Fabio; Noguera, Claudine Reports on Progress in Physics, Vol. 71, Issue 1 https://doi.org/10.1088/0034-4885/71/1/016501	journal	December 2007
Hypocoercivity for linear kinetic equations conserving mass Dolbeault, Jean; Mouhot, Clément; Schmeiser, Christian Transactions of the American Mathematical Society, Vol. 367, Issue 6 https://doi.org/10.1090/S0002-9947-2015-06012-7	journal	February 2015
Inhomogeneous Electron Gas Hohenberg, P.; Kohn, W. Physical Review, Vol. 136, Issue 3B, p. B864-B871 https://doi.org/10.1103/PhysRev.136.B864	journal	November 1964
Self-Consistent Equations Including Exchange and Correlation Effects Kohn, W.; Sham, L. J. Physical Review, Vol. 140, Issue 4A, p. A1133-A1138 https://doi.org/10.1103/PhysRev.140.A1133	journal	November 1965
Fast method for quantum mechanical molecular dynamics Niklasson, Anders M. N.; Cawkwell, Marc J. Physical Review B, Vol. 86, Issue 17 https://doi.org/10.1103/PhysRevB.86.174308	journal	November 2012
Extended Born-Oppenheimer Molecular Dynamics Niklasson, Anders M. N. Physical Review Letters, Vol. 100, Issue 12 https://doi.org/10.1103/PhysRevLett.100.123004	journal	March 2008
Unified Approach for Molecular Dynamics and Density-Functional Theory Car, R.; Parrinello, M. Physical Review Letters, Vol. 55, Issue 22 https://doi.org/10.1103/PhysRevLett.55.2471	journal	November 1985
Time-Reversible Born-Oppenheimer Molecular Dynamics Niklasson, Anders M. N.; Tymczak, C. J.; Challacombe, Matt Physical Review Letters, Vol. 97, Issue 12 https://doi.org/10.1103/PhysRevLett.97.123001	journal	September 2006
Iterative Procedures for Nonlinear Integral Equations Anderson, Donald G. Journal of the ACM, Vol. 12, Issue 4 https://doi.org/10.1145/321296.321305	journal	October 1965
Advanced Potential Energy Surfaces for Condensed Phase Simulation Demerdash, Omar; Yap, Eng-Hui; Head-Gordon, Teresa Annual Review of Physical Chemistry, Vol. 65, Issue 1 https://doi.org/10.1146/annurev-physchem-040412-110040	journal	April 2014
On the Poisson equation and diffusion approximation 3 Pardoux, E.; Veretennikov, A. Yu. The Annals of Probability, Vol. 33, Issue 3 https://doi.org/10.1214/009117905000000062	journal	May 2005
On the Poisson Equation and Diffusion Approximation. I Pardoux, E.; Veretennikov, Yu. The Annals of Probability, Vol. 29, Issue 3 https://doi.org/10.1214/aop/1015345596	journal	July 2001
On Poisson equation and diffusion approximation 2 Pardoux, È.; Veretennikov, A. Yu. The Annals of Probability, Vol. 31, Issue 3 https://doi.org/10.1214/aop/1055425774	journal	July 2003
Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics Lin, Lin; Lu, Jianfeng; Shao, Sihong Entropy, Vol. 16, Issue 1 https://doi.org/10.3390/e16010110	journal	December 2013
Hypoelliptic differential operators Hörmander, Lars Annales de l’institut Fourier, Vol. 11 https://doi.org/10.5802/aif.117	journal	January 1961

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