An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
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Publication:2482261
DOI10.1007/s10955-007-9470-2zbMath1214.82063MaRDI QIDQ2482261
Publication date: 16 April 2008
Published in: Journal of Statistical Physics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/s10955-007-9470-2
canonical ensemble; holonomic constraints; molecular dynamics; free energy calculation; hybrid Monte-Carlo
82C21: Dynamic continuum models (systems of particles, etc.) in time-dependent statistical mechanics
Uses Software
Cites Work
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- Markov chains and stochastic stability
- Comment on two distinct notions of free energy
- RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
- Manifolds, tensor analysis, and applications.
- The Nosé-Poincaré method for constant temperature molecular dynamics
- Symplectic numerical integrators in constrained Hamiltonian systems
- Exponential convergence of Langevin distributions and their discrete approximations
- Homogenization in time of singularly perturbed mechanical systems
- Energy-conserving integration of constrained Hamiltonian systems -- a comparison of approaches
- An unconstrained Hamiltonian formulation for incompressible fluid flow
- Markov chains for exploring posterior distributions. (With discussion)
- Mechanical integrators derived from a discrete variational principle
- Lie-Poisson Hamilton-Jacobi theory and Lie-Poisson integrators
- The discrete null-space method for the energy-consistent integration of constrained mechanical systems. I: Holonomic constraints
- Ergodicity for SDEs and approximations: locally Lipschitz vector fields and degenerate noise.
- Simulating Hamiltonian Dynamics
- Discrete mechanics and variational integrators
- The discrete null space method for the energy consistent integration of constrained mechanical systems. Part II: multibody dynamics
- Numerical Solution of Nonlinear Differential Equations with Algebraic Constraints II: Practical Implications
- Markov Chains
- Elastic rods, rigid bodies, quaternions and the last quadrature
- Optimal prediction and the Mori–Zwanzig representation of irreversible processes
- Theoretical and numerical comparison of some sampling methods for molecular dynamics
- A constrained hybrid Monte‐Carlo algorithm and the problem of calculating the free energy in several variables
- Statistical Mechanics of Fluid Mixtures
- Multi-multiplier ambient-space formulations of constrained dynamical systems, with an application to elastodynamics
- Monte Carlo strategies in scientific computing