What DF matrices are?

The analysis of the results of a MD simulation can performed using the Distance Fluctuation matrices (DF), based on the Coordination Propensity hypothesis:

low CP values, corresponding to low pair-distance fluctuations, highlight groups of residues that move in a mechanically coordinated way.

How to use the script

• Requisites

          - Python 3.0 (or newer version)

          - Numpy

          - Scipy

• Usage

The script can analyze a MD trajectory and identify the coordinated motions between residues. It can then filter the output matrix based on the distance to identify long-range coordinated motions.

The script can work both using only C-alphas (using either a pdb or a xyz file) or the sidechains (using a pdb file).

For more information run:

     python3 distance_fluctuation.py -h