ATD-Scripts is a a set of tools for automating simulations using the Anisotropic Thermal Diffusion method, in NAMD.
The methods are described in:
L. Martínez, A. C. M. Figueira, I. Polikarpov, M. S.Skaf, Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues. J. Phys. Chem. Lett. 2, 16, 2073-2078, 2011.
Further information: http://m3g.github.io/atd-scripts