<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="">it’s not that simple though..<div class="">in most of QMMM applications, you want your QM system be non-periodic. If you use MT (as in your input) you need indeed a much bigger box than the size strictly containing the QM atoms.</div><div class="">So, be wise in the use of a decoupling scheme that does not increase that much your box size requirements while still doing a good job in decoupling periodic images effectively.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 21 Apr 2016, at 13:24, <a href="mailto:jonas.va...@uantwerpen.be" class="">jonas.va...@uantwerpen.be</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thank you Teo for your response. I thought that by specifying the QM atoms in the input file (and by specifying a non-periodic box), the box-size didn't matter. I now decreased the QM box size, and this indeed worked. Thank you very much!<br class=""><br class="">Op donderdag 21 april 2016 06:14:38 UTC+2 schreef Teo:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div style="word-wrap:break-word" class=""><div class="">How can you expect that a QM simulation box of 25x25x25 gives the same time of a QMMM simulation where the QM box is 40x40x40?</div><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 20 Apr 2016, at 14:18, <a href="javascript:" target="_blank" gdf-obfuscated-mailto="_6JcTTSdLgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">jonas...@uantwerpen.be</a> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hi everybody! <br class=""><br class="">I am learning to use CP2K and I'm having some troubles with the set-up of my QM/MM simulations. My goal is to simulate the reactions of OH radicals with the central part of cytoglobin (metalloprotein). The central heme-group of the protein, together with an OH radical, make the QM part, whereas the rest of the protein (together with some surrounding water molecules) make the MM part. I first thermalized the structure (MM), and then (as a test) I performed some QM simulations (of only the central heme part + OH radical). I added the input file of this simulation in attachment (qm.inp). Now, I wanted to perform the real QM/MM simulations. However, these simulations run much slower (based on the output .ener file, the time per step increase from ~20s to ~120s) than the previous QM simulations. [I added this input file also in attachment (qmmm.inp).] In both cases I used CP2K version 2.5.1 and used 80 cores.<br class=""><br class="">I thought the idea of a QMMM simulation was that the speed of the entire simulation was determined by the QM part, so I don't understand what is slowing down my QMMM simulations. I tried a few things (e.g. changing embedding scheme from electrostatic to mechanical embedding), but none of the things I tried seemed to work. <br class=""><br class="">I hope one of you can tell me what I'm doing wrong, or can guide me to a possible solution. <br class=""><br class="">Thanks in advance!<br class=""><br class="">Best wishes,<br class="">Jonas Van der Paal<br class="">University of Antwerp (Belgium)<br class=""></div><div class=""><br class=""></div>
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