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Coarse-graining by Decimation of a PDB fileAim
The aim is to build a new Elastic Network Model from the initial classical Tirion model that still captures all the eseential features of the dynamics but iteratively eliminates atoms in such a way as to discard high-frequency modes.
In the Tirion model atoms are linked if their distance is less than a given threshold (radius).
To update this Network the following procedure is adpoted: individual frequencies are assigned to each atom, and, at each cycle, the atom with maximum frequency is eliminated. The links between its neighbours are re-defined and a new cycle begins until there remains a user-specified fraction of the initial number of atoms.
The method is derived from a renormalisation procedure initially derived in the statisticals physics of disordered materials and described by T. Garel and C. Monthus (PDF).
See here for an (Illustration).
You need a single input pdb file and the program will calculate the new links between the remaining atoms of the initial Elastic Network Model.
We recommand to proceed in two steps: first go though the Coarse-Graining procedure based on Names, or on the projection of the Hessian, before going to this step.
Input data formats
Page last modified 15:39 May 08, 2017.