Theoretical and numerical comparison of some sampling methods for molecular dynamics
From MaRDI portal
Computational methods for ergodic theory (approximation of invariant measures, computation of Lyapunov exponents, entropy, etc.) (37M25) Monte Carlo methods (65C05) Numerical analysis or methods applied to Markov chains (65C40) Dynamic continuum models (systems of particles, etc.) in time-dependent statistical mechanics (82C21)
Recommendations
- Some remarks on sampling methods in Molecular Dynamics
- Comparing the efficiencies of stochastic isothermal molecular dynamics methods
- Rational construction of stochastic numerical methods for molecular sampling
- Biomolecular sampling: algorithms, test molecules, and metrics
- A Metropolis adjusted Nosé-Hoover thermostat
Cites work
- A direct approach to conformational dynamics based on hybrid Monte Carlo
- A Hamiltonian Formulation for Recursive Multiple Thermostats in a Common Timescale
- An improved acceptance procedure for the hybrid Monte Carlo algorithm
- Backward Error Analysis for Numerical Integrators
- Biomolecular sampling: algorithms, test molecules, and metrics
- Cost of the generalised hybrid Monte Carlo algorithm for free field theory
- Discrete mechanics and variational integrators
- Ergodicity for SDEs and approximations: locally Lipschitz vector fields and degenerate noise.
- Exponential convergence of Langevin distributions and their discrete approximations
- Geometric convergence and central limit theorems for multidimensional Hastings and Metropolis algorithms
- Geometric Numerical Integration
- scientific article; zbMATH DE number 410743 (Why is no real title available?)
- scientific article; zbMATH DE number 46777 (Why is no real title available?)
- scientific article; zbMATH DE number 53679 (Why is no real title available?)
- scientific article; zbMATH DE number 976356 (Why is no real title available?)
- scientific article; zbMATH DE number 1082719 (Why is no real title available?)
- scientific article; zbMATH DE number 2152902 (Why is no real title available?)
- scientific article; zbMATH DE number 1851000 (Why is no real title available?)
- scientific article; zbMATH DE number 1405381 (Why is no real title available?)
- scientific article; zbMATH DE number 5049189 (Why is no real title available?)
- Isotropic hypoelliptic and trend to equilibrium for the Fokker-Planck equation with a high-degree potential
- Long-time averaging for integrable Hamiltonian dynamics
- Markov chains and stochastic stability
- Molecular modeling and simulation. An interdisciplinary guide
- Monte Carlo sampling methods using Markov chains and their applications
- Monte Carlo strategies in scientific computing
- Monte-Carlo methods for the transport and diffusion equations
- Non-ergodicity of the Nosé-Hoover thermostatted harmonic oscillator
- Optimal Scaling of Discrete Approximations to Langevin Diffusions
- Probability and random processes.
- Projection of diffusions on submanifolds: Application to mean force computation
- Quasi-symplectic methods for Langevin-type equations
- Rates of convergence of the Hastings and Metropolis algorithms
- Second-order discretization schemes of stochastic differential systems for the computation of the invariant law
- Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
- Simulating Hamiltonian Dynamics
- Smooth Transition Densities for One-Dimensional Diffusions
- Splitting for Dissipative Particle Dynamics
- Stability of Markovian processes II: continuous-time processes and sampled chains
- Stochastic differential equations and applications.
- Sur quelques algorithmes récursifs pour les probabilités numériques
- The Art of Molecular Dynamics Simulation
- The Nosé-Poincaré method for constant temperature molecular dynamics
- The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method
Cited in
(58)- Theory and algorithms for mixed Monte Carlo-stochastic dynamics simulations
- Predictive coarse-graining
- Palindromic 3-stage splitting integrators, a roadmap
- Irreducibility and geometric ergodicity of Hamiltonian Monte Carlo
- Two-scale coupling for preconditioned Hamiltonian Monte Carlo in infinite dimensions
- Continuum limit and preconditioned Langevin sampling of the path integral molecular dynamics
- HMC: reducing the number of rejections by not using leapfrog and some results on the acceptance rate
- Mixing of Hamiltonian Monte Carlo on strongly log-concave distributions: continuous dynamics
- On the geometric ergodicity of Hamiltonian Monte Carlo
- Hybrid Monte Carlo methods for sampling probability measures on submanifolds
- Optimal tuning of the hybrid Monte Carlo algorithm
- On the rate of convergence to equilibrium of the Andersen thermostat in molecular dynamics
- An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
- Numerical algorithms for stationary statistical properties of dissipative dynamical systems
- Efficient numerical evaluation of thermodynamic quantities on infinite (semi-)classical chains
- Adaptive thermostats for noisy gradient systems
- The computation of averages from equilibrium and nonequilibrium Langevin molecular dynamics
- Langevin molecular dynamics derived from Ehrenfest dynamics
- Low temperature dynamics of the one-dimensional discrete nonlinear Schrödinger equation
- Implicit mass-matrix penalization of Hamiltonian dynamics with application to exact sampling of stiff systems
- A stochastic phase-field model determined from molecular dynamics
- Approximation of stationary statistical properties of dissipative dynamical systems: time discretization
- A Conjecture about Molecular Dynamics
- Free energy computations by minimization of Kullback-Leibler divergence: An efficient adaptive biasing potential method for sparse representations
- A patch that imparts unconditional stability to explicit integrators for Langevin-like equations
- Monte Carlo sampling in diffusive dynamical systems
- Rational construction of stochastic numerical methods for molecular sampling
- Weighted \(L^2\)-contractivity of Langevin dynamics with singular potentials
- Geometric Integration of Measure-Preserving Flows for Sampling
- Connecting the Dots: Numerical Randomized Hamiltonian Monte Carlo with State-Dependent Event Rates
- scientific article; zbMATH DE number 7561278 (Why is no real title available?)
- Hypocoercivity properties of adaptive Langevin dynamics
- Symmetrically processed splitting integrators for enhanced Hamiltonian Monte Carlo sampling
- A Metropolis adjusted Nosé-Hoover thermostat
- Geometric integrators and the Hamiltonian Monte Carlo method
- Metropolis integration schemes for self-adjoint diffusions
- Molecular Simulation in the Canonical Ensemble and Beyond
- Some remarks on sampling methods in Molecular Dynamics
- Biomolecular sampling: algorithms, test molecules, and metrics
- Temperature–energy-space sampling molecular dynamics: deterministic and single-replica method utilizing continuous temperature system
- A Micro-Macro Markov Chain Monte Carlo Method for Molecular Dynamics using Reaction Coordinate Proposals
- Finite-temperature coarse-graining of one-dimensional models: mathematical analysis and computational approaches
- Convergence of nonequilibrium Langevin dynamics for planar flows
- Geometric Ergodicity for Hamiltonian Monte Carlo on Compact Manifolds
- Convergence of unadjusted Hamiltonian Monte Carlo for mean-field models
- Comparing the efficiencies of stochastic isothermal molecular dynamics methods
- Sampling algorithms in statistical physics: a guide for statistics and machine learning
- Computational efficiency study of a micro-macro Markov chain Monte Carlo method for molecular dynamics
- Weak error expansion of a numerical scheme with rejection for singular Langevin process
- An external dual charge approach to the multimarginal optimal transport with Coulomb cost
- Finite sampling interval effects in Kramers-Moyal analysis
- Unbiasing Hamiltonian Monte Carlo algorithms for a general Hamiltonian function
- Unadjusted Hamiltonian MCMC with stratified Monte Carlo time integration
- Extra chance generalized hybrid Monte Carlo
- Numerical stability revisited: a family of benchmark problems for the analysis of explicit stochastic differential equation integrators
- Equilibrium sampling from nonequilibrium dynamics
- Weak backward error analysis for Langevin process
- Path sampling with stochastic dynamics: some new algorithms
This page was built for publication: Theoretical and numerical comparison of some sampling methods for molecular dynamics
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5447907)