A. Fischer, Ch. Schutte, P. Deuflhard, and F. Cordes. Hierarchical uncoupling-coupling of metastable conformations. Technical report, ZIB, 2001. Home/Search Document Details and Download
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Visualizing Dynamic Molecular Conformations - Schmidt-Ehrenberg, Baum, Hege (2002) (Correct)
....the next trajectory on base of the endpoint of the previous trajectory, guaranteeing that the states x i (i = 1, M tot ) are distributed according to the density fcan . The Hybrid Monte Carlo technique employed for generation of the molecular configurations used in this paper is described in [7]. 3.3 Conformation Analysis The phrase metastable conformation indicates a dynamic aspect of molecular behavior: it denotes metastable shapes, i.e. molecular geometries which survive the fast oscillations around equilibrium positions, this means configurations whose trajectory remains inside a ....
Alexander Fischer, Christof Sch utte, Peter Deuflhard, and Frank Cordes. Hierarchical uncoupling-coupling of metastable conformations. In Tamar Schlick and Hin Hark Gan, editors, Computational Methods for Macromolecules: Challenges and Applications, Proc. 3rd Int. Workshop on Algorithms for Macromolecular Modeling, New York, Oct. 2000.
Dominant Paths between Almost Invariant Sets of.. - Preis, Dellnitz.. Self-citation (Schutte) (Correct)
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A. Fischer, Ch. Schutte, P. Deuflhard, and F. Cordes. Hierarchical uncoupling-coupling of metastable conformations. Technical report, ZIB, 2001.
Extracting Macroscopic Stochastic Dynamics: Model Problems - Huisinga, Schütte, Stuart (2003) (1 citation) Self-citation (Schtte) (Correct)
.... We emphasize, however, that the dimension of X may sometimes be so high as to make the transfer operator approach to the identification of # computationally infeasible if naively applied directly in X ; this issue can be ameliorated to some extent by the use of adaptive algorithms such as those in [4, 8], but for many problems in high dimensions, combining the transfer operator approach with simpler clustering approaches and or mathematical modeling, such as the exploitation of fast slow time scale separation, may be needed to identify #. In order to study question (Q2) we will assume that # is ....
Fischer, A.; Schtte, C.; Deuflhard, P.; Cordes. F. Hierarchical uncoupling-coupling of metastable conformations. Computational methods for macromolecules: challenges and applications---Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling. Lecture Notes in Computational Science and Engineering. Springer, 2002.
Metastable Conformations via successive.. - Cordes, Weber.. (2002) (1 citation) Self-citation (Cordes) (Correct)
....to [5] of T for a given discretization A 1 , AN one can find the number s of conformations C 1 , C s and s pairwise disjoint index sets I(i) N such that C i = j#I(i) A j . A main advantage of the metastability analysis is used in more e#cient sampling methods [8]. Since critical slowing down of simulations, either Molecular Dynamics or Monte Carlo, is strongly connected with metastability, the decomposition of conformational space can be used to uncouple the sampling into simulations within separate subsets. Combined with a hierarchical temperature or ....
....slowing down, if all metastable conformations have been identified. Therefore, convergence of resimulation serves as an a posteriori criterion for the quality of metastability analysis. Moreover, resimulation is combined with a hierachical embedding protocol introduced in previous publications [8]. Starting the simulation at high temperature facilitates the crossing of energy barriers and improves convergence. After analysis of metastability, resimulation is started as a bridge sampling between the initial high and a new, lower temperature. The parameters for bridge sampling are ....
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A. Fischer, C. Schtte, P. Deuflhard, and F. Cordes. Hierarchical uncoupling-coupling of metastable conformations. In T. Schlick and H.H. Gan, editors, Computational methods for macromolecules: Challenges and applications, Proceedings of the third international workshop on algorithms for macromolecular modeling, pages 235--261. Springer, 2002.
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