Biomolecular sampling: algorithms, test molecules, and metrics

MaRDI QIDQ5484137zbMATH OpenFDO

Authors Scott S. Hampton, Paul Brenner, Aaron Wenger, Santanu Chatterjee, Jesús A. Izaguirre

Publication date 24 August 2006

zbMATH Keywords

Langevin impulsemolecular dynamicsNosé-Hoover dynamicsreplica exchangeShadow Hybrid Monte Carlo

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Applications of statistical mechanics to specific types of physical systems (82D99) Computational methods for problems pertaining to biology (92-08) Biophysics (92C05) Biochemistry, molecular biology (92C40)

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Cited in

(4)

• Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
• Adaptive conformational sampling based on replicas
• Theoretical and numerical comparison of some sampling methods for molecular dynamics
• Application of biased Metropolis algorithms: from protons to proteins

Describes a project that uses

Uses Software

• ProtoMol

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