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Computation of Essential Molecular Dynamics by Subdivision Techniques I: Basic Concept

Please always quote using this URN: urn:nbn:de:0297-zib-2553
  • The paper presents the concept of a new type of algorithm for the numerical computation of what the authors call the {\em essential dynamics\/} of molecular systems. Mathematically speaking, such systems are described by Hamiltonian differential equations. In the bulk of applications, individual trajectories are of no specific interest. Rather, time averages of physical observables or relaxation times of conformational changes need to be actually computed. In the language of dynamical systems, such information is contained in the natural invariant measure (infinite relaxation time) or in almost invariant sets ("large" finite relaxation times). The paper suggests the direct computation of these objects via eigenmodes of the associated Frobenius-Perron operator by means of a multilevel subdivision algorithm. The advocated approach is different to both Monte-Carlo techniques on the one hand and long term trajectory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are just structurally connected via the underlying Frobenius-Perron theory. Numerical experiments with a first version of our suggested algorithm are included to illustrate certain distinguishing properties. A more advanced version of the algorithm will be presented in a second part of this paper.

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Author:Peter Deuflhard, Michael Dellnitz, Oliver Junge, Christof Schütte
Document Type:ZIB-Report
Date of first Publication:1996/11/28
Series (Serial Number):ZIB-Report (SC-96-45)
Published in:Appeared in: P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, R.D. Skeel (eds.), Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, 4, Springer-Verlag, 98-115, 1998
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