A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations

DOI10.1007/978-3-642-32979-1_9zbMath1269.82072OpenAlexW1548146254MaRDI QIDQ2838321

Alexander Bujotzek, Konstantin Fackeldey, Marcus Weber

Publication date: 9 July 2013

Published in: Meshfree Methods for Partial Differential Equations VI (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-642-32979-1_9

zbMATH Keywords

molecular dynamicspartition of unitytransfer operatorMarkovianityconformation dynamicsrobust Perron cluster analysis

Mathematics Subject Classification ID

Related Items (2)

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification ⋮ \textsf{ZIBgridfree}: efficient conformational analysis by partition-of-unity coupling

Uses Software

• Amira
• Gromacs
• ZIBgridfree
• LINCS
• ZIBAmira

Cites Work

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• A direct approach to conformational dynamics based on hybrid Monte Carlo
• Robust Perron cluster analysis in conformation dynamics
• On the Approximation Quality of Markov State Models
• Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

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