Institute of Chemistry - University of Campinas

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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.

Link: [Paper] [Supplementary Information]

The scripts are provided free of any charge. Please cite this article if these scripts were useful.

If you have any problem, comment or suggestion regarding this package, please contact Leandro Martínez at

Computing thermal couplings from PDB files directly via network models:

The scripts required to compute the thermal couplings using network model representations of the protein structure are available at: These methods are described in:
L. Censoni, H. S. Muniz, L. Martínez, A network model predicts the intensity of residue-protein thermal coupling, Bioinformatics, 2017. [LINK]

See also:
Author's software page
The TANGO project