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Title: Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

Journal Article · · Journal of Chemical Physics
DOI:https://doi.org/10.1063/1.4978684· OSTI ID:1414137
 [1];  [2];  [3]; ORCiD logo [4];  [5];  [1]
  1. Univ. of Southampton, Southampton (United Kingdom)
  2. Univ. of Southampton, Southampton (United Kingdom); Gdansk Univ. of Technology, Gdansk (Poland)
  3. Univ. of California, Berkeley, CA (United States)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes - in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC). Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
AC52-06NA25396; AC02-05CH11231; LANL2014E8AN
OSTI ID:
1414137
Alternate ID(s):
OSTI ID: 1476472; OSTI ID: 1989961
Report Number(s):
LA-UR-17-20731; TRN: US1800661
Journal Information:
Journal of Chemical Physics, Vol. 146, Issue 12; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 25 works
Citation information provided by
Web of Science

References (84)

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules journal August 2011
A simple polarizable model of water based on classical Drude oscillators journal September 2003
Polarization effects in molecular mechanical force fields journal July 2009
Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born–Oppenheimer trajectories journal December 2004
Ab initio molecular dynamics: Analytically continued energy functionals and insights into iterative solutions journal August 1992
Current Status of the AMOEBA Polarizable Force Field journal March 2010
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data journal November 2012
Self-consistent first-principles technique with linear scaling journal April 1995
Special Issue on Polarization journal October 2007
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation journal May 2003
Linear scaling conjugate gradient density matrix search as an alternative to diagonalization for first principles electronic structure calculations journal April 1997
Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations journal December 2008
Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals journal June 2001
Fock matrix dynamics journal March 2004
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model journal September 2014
An effective fragment method for modeling solvent effects in quantum mechanical calculations journal August 1996
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics journal October 2014
Accurate ionic forces and geometry optimization in linear-scaling density-functional theory with local orbitals journal May 2011
Geometric integration in Born-Oppenheimer molecular dynamics journal December 2011
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ Atoms journal November 2014
Linear-scaling symmetric square-root decomposition of the overlap matrix journal March 2007
Density functional tight binding
  • Elstner, Marcus; Seifert, Gotthard
  • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2011 https://doi.org/10.1098/rsta.2012.0483
journal March 2014
Advanced Potential Energy Surfaces for Condensed Phase Simulation journal April 2014
Nearsightedness of electronic matter journal August 2005
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field journal September 2016
Introducing ONETEP : Linear-scaling density functional simulations on parallel computers journal February 2005
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction journal November 2015
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests journal October 2002
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations journal October 2002
Daubechies wavelets for linear scaling density functional theory journal May 2014
Accelerated, energy-conserving Born–Oppenheimer molecular dynamics via Fock matrix extrapolation journal January 2005
Molecular dynamics simulations at constant pressure and/or temperature journal February 1980
Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics—Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections journal March 2012
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases journal July 2001
A molecular dynamics method for simulations in the canonical ensemble journal January 2002
Molecular dynamics without effective potentials via the Car-Parrinello approach journal August 1990
The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water journal August 2014
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation journal June 2009
Calculation of the Free Energy of Polarization:  Quantifying the Effect of Explicitly Treating Electronic Polarization on the Transferability of Force-Field Parameters journal June 2007
Network equilibration and first-principles liquid water journal January 2004
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins journal August 2013
ONETEP: linear-scaling density-functional theory with plane-waves journal February 2006
Recent progress in linear scaling ab initio electronic structure techniques journal March 2002
Hybrid atomistic simulation methods for materials systems journal January 2009
Molecular and Atomic Polarizabilities:  Thole's Model Revisited journal April 1998
Efficient treatment of induced dipoles journal August 2015
ReaxFF:  A Reactive Force Field for Hydrocarbons journal October 2001
Enhanced semiempirical QM methods for biomolecular interactions journal January 2015
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations journal March 1999
Polymorphic transitions in single crystals: A new molecular dynamics method journal December 1981
A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability journal January 2010
Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules : I. Theory journal January 1969
Pulay forces from localized orbitals optimized in situ using a psinc basis set journal June 2012
Molecular dynamics simulations of biomolecules journal September 2002
Electronic-structure calculations and molecular-dynamics simulations with linear system-size scaling journal August 1994
Semiempirical GGA-type density functional constructed with a long-range dispersion correction journal January 2006
Local structure analysis in ab initio liquid water journal July 2015
Fast evaluation of polarizable forces journal October 2005
Efficient recursion method for inverting an overlap matrix journal October 2001
Development of transferable interaction models for water. IV. A flexible, all-atom polarizable potential (TTM2-F) based on geometry dependent charges derived from an ab initio monomer dipole moment surface journal January 2002
Development of a Polarizable Force Field Using Multiple Fluctuating Charges per Atom journal February 2010
Explicit reversible integrators for extended systems dynamics journal April 1996
Density kernel optimization in the ONETEP code journal June 2008
Cutoff Errors in the Ewald Summation Formulae for Point Charge Systems journal January 1992
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field journal July 2016
Systematic Improvement of a Classical Molecular Model of Water journal August 2013
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
Perspective: How good is DFT for water? journal April 2016
Building Force Fields: An Automatic, Systematic, and Reproducible Approach journal May 2014
RETRACTED ARTICLE: ONETEP: linear-scaling density-functional theory with plane-waves journal June 2007
A molecular dynamics method for simulations in the canonical ensemble journal June 1984
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations text January 1999
Structure and dynamics of liquid water from ab initio molecular dynamics-comparison of BLYP, PBE, and revPBE density functionals with and without van der Waals corrections text January 2012
Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules: II. Force constants of water journal April 1970
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation text January 2009
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density text January 1988
The Individual and Collective Effects of Exact Exchange and Dispersion Interactions on the Ab Initio Structure of Liquid Water text January 2014
Generalized Extended Lagrangian Born-Oppenheimer Molecular Dynamics text January 2014
Local Structure Analysis in $Ab$ $Initio$ Liquid Water text January 2015
Efficient Recursion Method for Inverting Overlap Matrix text January 2001
Network equilibration and first-principles liquid water text January 2004
Nearsightedness of Electronic Matter text January 2005
Electronic structure calculations and molecular dynamics simulations with linear system-size scaling text January 1994

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