Multiple-time-stepping generalized hybrid Monte Carlo methods

DOI10.1016/J.JCP.2014.08.052MaRDI QIDQ349691zbMATH OpenOpenAlexFDO

Authors Bruno Escribano, Elena Akhmatskaya, Sebastian Reich, Jon M. Azpiroz

Publication date 5 December 2016

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

Full work available at URL http://hdl.handle.net/20.500.11824/166

zbMATH Keywords

mollificationmolecular dynamicsforce splittinggeneralized hybrid Monte Carlomodified Hamiltonians

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31) Discretization methods and integrators (symplectic, variational, geometric, etc.) for dynamical systems (37M15)

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• Computational Science - ICCS 2004

Cites work

• scientific article; zbMATH DE number 46777 (Why is no real title available?)
• scientific article; zbMATH DE number 1745051 (Why is no real title available?)
• A comparison of generalized hybrid Monte Carlo methods with and without momentum flip
• Combining stochastic and deterministic approaches within high efficiency molecular simulations
• Cost of the generalised hybrid Monte Carlo algorithm for free field theory
• Error and timing analysis of multiple time-step integration methods for molecular dynamics
• GSHMC: An efficient method for molecular simulation
• Long-Time-Step Methods for Oscillatory Differential Equations
• Molecular dynamics and the accuracy of numerically computed averages
• Molecular modeling and simulation. An interdisciplinary guide
• Monte Carlo strategies in scientific computing
• Optimal tuning of the hybrid Monte Carlo algorithm
• Practical construction of modified Hamiltonians
• ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
• Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
• The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method

Cited in

(11)

• Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
• Adaptive multi-stage integration schemes for Hamiltonian Monte Carlo
• Combining stochastic and deterministic approaches within high efficiency molecular simulations
• scientific article; zbMATH DE number 2050851 (Why is no real title available?)
• Multi-stage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods
• GSHMC: An efficient method for molecular simulation
• Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
• The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method
• Implicit mass-matrix penalization of Hamiltonian dynamics with application to exact sampling of stiff systems
• A comparison of generalized hybrid Monte Carlo methods with and without momentum flip
• Thread-parallel anisotropic mesh adaptation

Describes a project that uses

Uses Software

• ProtoMol
• GSHMC

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