[DFTB-Plus-User] analyzing MD calculations

[Alessandro Pirrotta]

Dear Yunlong,

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Best regards,
Alessandro Pirrotta

> On 22 Nov 2017, at 09.04, Yunlong <yunlongliao at gmail.com> wrote:
> 
> please stop send me email anymore.
> thanks
> 
>> On Mon, Nov 20, 2017 at 3:10 PM, 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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>> 
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> 
> 
> 
> -- 
> Yunlong Liao
> Department of Physics, University of Puerto Rico
> Río Piedras Campus, San Juan, PR  (757) 690-0607
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