Coupling overall rotations with modal dynamics |
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Authors: | J Elezgaray G Marcou Y H Sanejouand |
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Institution: | (1) Centre de Recherche Paul Pascal, Avenue Schweitzer, 33600 Pessac, France, FR |
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Abstract: | We consider a model for protein dynamics in which only certain collective, global motions are allowed. These directions are
given by the slowest harmonics modes, as given in the reference frame of the protein. Furthermore, the latter is allowed to
rotate and translate in response to interactions with other molecules. The model is obtained by projecting the (averaged)
Newton equations onto this set of harmonic modes. We show that the subsequent homogenization of the time scales allows time
steps one order of magnitude larger than the standard ones. This homogenization is also shown to be a necessary ingredient
in order to get meaningful statistics of the trajectory.
Received: 3 July 2000 / Accepted: 15 September 2000 / Published online: 21 December 2000 |
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Keywords: | : Normal mode Large time step Molecular dynamics Protein |
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