\textsf{ZIBgridfree}: efficient conformational analysis by partition-of-unity coupling

DOI10.1007/S10910-013-0265-1MaRDI QIDQ460863zbMATH OpenOpenAlexFDO

Authors Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber

Publication date 9 October 2014

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10910-013-0265-1

zbMATH Keywords

molecular simulationmeshfree methodsconformational analysis

Mathematics Subject Classification ID

Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Software, source code, etc. for problems pertaining to information and communication theory (94-04)

Recommendations

• Meshless methods in conformation dynamics
• Adaptive conformational sampling based on replicas
• A direct approach to conformational dynamics based on hybrid Monte Carlo
• A central partition of molecular conformational space. III. Combinatorial determination of the volume spanned by a molecular system
• A meshless discretization method for Markov state models applied to explicit water peptide folding simulations

Cites work

• scientific article; zbMATH DE number 2133743 (Why is no real title available?)
• A Relationship Between Arbitrary Positive Matrices and Doubly Stochastic Matrices
• A meshless discretization method for Markov state models applied to explicit water peptide folding simulations
• Inference from iterative simulation using multiple sequences
• Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations
• Meshless methods in conformation dynamics
• On the approximation quality of Markov state models
• Robust Perron cluster analysis in conformation dynamics
• Stable Computation of Probability Densities for Metastable Dynamical Systems

Cited in

(3)

• A central partition of molecular conformational space. IV: Extracting information from the graph of cells
• ZIBMolPy
• Meshless methods in conformation dynamics

Describes a project that uses

Uses Software

• Gromacs
• ZIBgridfree
• ACPYPE

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