Coupling overall rotations with modal dynamics
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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.
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