<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 07 Jul 2015, at 23:48, Vojtech Mlynsky <<a href="mailto:vojtech...@gmail.com" class="">vojtech...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear cp2k users.<div class=""><br class=""></div><div class="">I would like to run QM/MM calculation using CP2K code.</div><div class="">I need to cut covalent bonds in my system, which requires usage of link atoms.</div><div class=""><br class=""></div><div class="">I am not sure, if I understood correctly the way how to specify them (section LINK).</div><div class=""><br class=""></div><div class="">The keywords are:</div><div class="">QM_INDEX --> should that be the index of QM atom at the QM / MM boundary.</div><div class="">MM_INDEX --> index of MM atom at the QM / MM boundary</div><div class="">QM_KIND --> type of link atom substituting MM atom specified by MM index.</div><div class=""><br class=""></div><div class="">Is that right?</div><div class=""><br class=""></div></div></div></blockquote>correct</div><div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">Are there other 'tricky things' that need to be specified? For example, does it matter which bonds (i.e., C - C, C - N,..) are cut, or the code will adjust that automatically? </div></div></div></blockquote><div><br class=""></div>standard QM/MM good sense apply. The code does not do anything automatically.</div><div><br class=""></div><div>One more thing: you’ll have to specify the ratio between the classical equilibrium bond distance and the quantum one (with the kinds that you have specified).</div><div><br class=""></div><div>Teo</div><div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><div class="">Thanks in advance for reply.</div><div class=""><br class=""></div><div class="">Vojtech.</div></div><div class=""><br class="webkit-block-placeholder"></div>
-- <br class="">
You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" class="">cp2k+uns...@googlegroups.com</a>.<br class="">
To post to this group, send email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class="">
Visit this group at <a href="http://groups.google.com/group/cp2k" class="">http://groups.google.com/group/cp2k</a>.<br class="">
For more options, visit <a href="https://groups.google.com/d/optout" class="">https://groups.google.com/d/optout</a>.<br class="">
</div></blockquote></div><br class=""></body></html>