<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div><span></span></div><div><div><span></span></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8">Dear Yunlong,<div><br></div><div>If you wish to unsubscribe from the DFTB+ mailing list you can do so at the following link: <a href="https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user">https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user</a><br><br><div><div style="direction: inherit;">Best regards,</div><div style="direction: inherit;">Alessandro Pirrotta</div></div><div><br>On 22 Nov 2017, at 09.04, Yunlong <<a href="mailto:yunlongliao@gmail.com">yunlongliao@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">please stop send me email anymore.<div>thanks</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 20, 2017 at 3:10 PM, Andrea Pedrielli <span dir="ltr"><<a href="mailto:andrea.pedrielli@unitn.it" target="_blank">andrea.pedrielli@unitn.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi, <div>if you dump xyz files OVITO code can be used to visualize the DFTB output and to compute bond connectivity and RDF   <a href="https://ovito.org/" target="_blank">https://ovito.org/</a> <div><div>There is the possibility to use the software from a python interface to repeat boring instructions.</div><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">Andrea</font></span><div><div class="h5"><br><div><br>Il lunedì 20 novembre 2017, juhasz.g.aa <<a href="mailto:juhasz.g.aa@m.titech.ac.jp" target="_blank">juhasz.g.aa@m.titech.ac.jp</a>> ha scritto:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
I am looking for analyzing some MD simulations, however I fast realized I lacking many of the tools (and also lacking experience in MD).<br>
<br>
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...<br>
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.<br>
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.<br>
<br>
Thank you for your kind help in forward.<br>
Gergely Juhasz<br>
Tokyo Institute of Technology<br>
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<a href="https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user" rel="noreferrer" target="_blank">https://mailman.zfn.uni-<wbr>bremen.de/cgi-bin/mailman/<wbr>listinfo/dftb-plus-user</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div style="text-align:center">Yunlong Liao</div>
<div style="text-align:center">Department of Physics, University of Puerto Rico</div>
<div style="text-align:center">Río Piedras Campus, San Juan, PR <b> (757) 690-0607</b></div></div></div></div></div>
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