[DFTB-Plus-User] analyzing MD calculations

[Jacek Jakowski]

you can use  VMD  and    choose  "dynamic bonds"  representation  which
allows to  set a  cutoff  for  bond length.

Jacek

On Mon, Nov 20, 2017 at 2:10 AM, Andrea Pedrielli <andrea.pedrielli at unitn.it
> wrote:

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