The Nosé-Poincaré method for constant temperature molecular dynamics

DOI10.1006/jcph.1998.6171zbMath0933.81058OpenAlexW2040681130MaRDI QIDQ1305949

Brian B. Laird, Benedict J. Leimkuhler, Stephen D. Bond

Publication date: 4 April 2000

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1006/jcph.1998.6171

zbMATH Keywords

numerical experimentsHamiltonian systemconstant temperature molecular dynamicsNosé-Poincaré methodsymplectic discretization method

Mathematics Subject Classification ID

Computational methods for problems pertaining to quantum theory (81-08) Geometry and quantization, symplectic methods (81S10) Molecular physics (81V55)

Related Items (24)

Nosé–Hoover nonequilibrium dynamics and statistical mechanics ⋮ Generalized-ensemble algorithms for molecular dynamics simulations ⋮ Multibaric–multithermal molecular dynamics simulation: generalized Nosé–Poincaré–Andersen method ⋮ Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules ⋮ Thermostat for a relativistic gas ⋮ Hamiltonian thermostats fail to promote heat flow ⋮ Invariant tori for multi-dimensional integrable Hamiltonians coupled to a single thermostat ⋮ Non-ergodicity of the Nosé-Hoover thermostatted harmonic oscillator ⋮ Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats ⋮ Overcoming the timescale barrier in molecular dynamics: Transfer operators, variational principles and machine learning ⋮ Multi-scale modeling of surface effects in nano-materials with temperature-related Cauchy-Born hypothesis via the modified boundary Cauchy-Born model ⋮ Least square method for the calculation of elastic constants ⋮ Ergodicity of a singly-thermostated harmonic oscillator ⋮ Nonautonomous Hamiltonian quantum systems, operator equations, and representations of the Bender-Dunne Weyl-ordered basis under time-dependent canonical transformations ⋮ General purpose molecular dynamics simulations fully implemented on graphics processing units ⋮ On the rate of convergence to equilibrium of the Andersen thermostat in molecular dynamics ⋮ On the estimation and correction of discretization error in molecular dynamics averages ⋮ An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics ⋮ Modified Nosé-Hoover thermostat for solid state for constant temperature molecular dynamics simulation ⋮ A Metropolis adjusted Nosé-Hoover thermostat ⋮ Molecular Simulation in the Canonical Ensemble and Beyond ⋮ Theoretical and numerical comparison of some sampling methods for molecular dynamics ⋮ Torsion and bending periodic boundary conditions for modeling the intrinsic strength of nanowires ⋮ Generalized mathematical homogenization: From theory to practice

Cites Work

• Symplectic numerical integrators in constrained Hamiltonian systems
• Momentum conserving symplectic integrators
• Variable time step integration with symplectic methods
• Variable steps for reversible integration methods
• On the Hamiltonian interpolation of near-to-the-identity symplectic mappings with application to symplectic integration algorithms
• Equivariant constrained symplectic integration
• Time transformations in the extended phase-space
• Backward Error Analysis for Numerical Integrators
• Explicit Lie-Poisson integration and the Euler equations
• Symplectic Partitioned Runge–Kutta Methods for Constrained Hamiltonian Systems
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