A direct approach to conformational dynamics based on hybrid Monte Carlo

DOI10.1006/jcph.1999.6231zbMath0933.65145OpenAlexW2046290306MaRDI QIDQ1305955

Christof Schütte, Wilhelm Huisinga, Alexander Fischer, Peter Deuflhard

Publication date: 30 March 2000

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

Full work available at URL: https://semanticscholar.org/paper/f51c818cb2dae477aafee27898f163804b80097e

zbMATH Keywords

numerical examplesHamiltonian systemsdynamical systemFrobenius-Perron operatorMarkov operatormolecular dynamicstransition operatortransition probabilitiesconformationstochastic matrixdynamical stabilityreweightingbiomolecular systemsconformational dynamicsessential degrees of freedomhybrid Monte Carlo techniques

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Dynamical systems in biology (37N25) Dynamical systems in other branches of physics (quantum mechanics, general relativity, laser physics) (37N20) Numerical methods for Hamiltonian systems including symplectic integrators (65P10) Discretization methods and integrators (symplectic, variational, geometric, etc.) for dynamical systems (37M15)

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Uses Software

• GROMOS

Cites Work

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• Markov chains and stochastic stability
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• Lie-Poisson Hamilton-Jacobi theory and Lie-Poisson integrators
• Statistical Analysis of Circular Data
• A correlation coefficient for circular data
• On the Approximation of Complicated Dynamical Behavior
• An Improved Spectral Graph Partitioning Algorithm for Mapping Parallel Computations

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