[DFTB-Plus-User] analyzing MD calculations

Andrea Pedrielli andrea.pedrielli at unitn.it
Mon Nov 20 08:10:04 CET 2017

if you dump xyz files OVITO code can be used to visualize the DFTB output
and to compute bond connectivity and RDF   https://ovito.org/
There is the possibility to use the software from a python interface to
repeat boring instructions.


Il lunedì 20 novembre 2017, juhasz.g.aa <juhasz.g.aa at m.titech.ac.jp> ha

> Dear all,
> I am looking for analyzing some MD simulations, however I fast realized I
> lacking many of the tools (and also lacking experience in MD).
> Can anyone recommend a toolkit or software that can help me in calculation
> radial distribution functions and connectivity tables to analyze DFTB+ MD
> outputs? I would like to find eg. absorption or reaction steps on
> surfaces...
> I have a hard time especially with calculating and analyzing connectivity,
> the free tools I found were made to classical MD simulations on protein and
> such, using the same connectivity throughout the calculation from input PDB
> file.
> Now I understand I can just code many of these myself, but if there are
> tools for that it would save me a lot of sweat and tears.
> Thank you for your kind help in forward.
> Gergely Juhasz
> Tokyo Institute of Technology
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