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

molecular dynamicsreplica exchangeNosé-Hoover dynamicsLangevin impulseShadow Hybrid Monte Carlo

Mathematics Subject Classification ID

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

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Cited in

(4)

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

Describes a project that uses

Uses Software

• ProtoMol

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