T
Thomas E. Cheatham
Researcher at University of Utah
Publications - 164
Citations - 38522
Thomas E. Cheatham is an academic researcher from University of Utah. The author has contributed to research in topics: Molecular dynamics & Nucleic acid. The author has an hindex of 58, co-authored 156 publications receiving 32976 citations. Previous affiliations of Thomas E. Cheatham include Free University of Berlin & University of California, San Francisco.
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Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.
TL;DR: There is no one perfect "one size fits all" algorithm for clustering MD trajectories and that the results strongly depend on the choice of atoms for the pairwise comparison, so the best performance was observed with the average-linkage, means, and SOM algorithms.
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Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
InSuk Joung,Thomas E. Cheatham +1 more
TL;DR: The correlations among the various properties led to the following conclusions: (1) the reliability of the ion force fields is significantly affected by the specific choice of water model, and (2) Ion−ion interactions are very important to accurately simulate the properties, especially solubility.
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The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
TL;DR: The flying ice cube problem as mentioned in this paper occurs when velocity rescaling using standard protocols can systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees of freedom.
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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
Marie Zgarbová,Jiří Šponer,Jiří Šponer,Michal Otyepka,Thomas E. Cheatham,Rodrigo Galindo-Murillo,Petr Jurečka +6 more
TL;DR: A refinement of this potential, β(OL1), which was derived using the recently introduced methodology that includes conformation-dependent solvation effects, significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone.
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Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.
TL;DR: An overview of the experiences, some cautionary notes, and recommendations for further study in molecular dynamics simulation of nucleic acids are provided.