[CP2K:7698] Setting up QMMM simulation (much slower than QM part only)

jonas.va... at uantwerpen.be jonas.va... at uantwerpen.be
Thu Apr 21 13:24:32 CEST 2016


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!

Op donderdag 21 april 2016 06:14:38 UTC+2 schreef Teo:
>
> 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?
>
>
> On 20 Apr 2016, at 14:18, jonas... at uantwerpen.be <javascript:> wrote:
>
> Hi everybody! 
>
> 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.
>
> 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. 
>
> I hope one of you can tell me what I'm doing wrong, or can guide me to a 
> possible solution. 
>
> Thanks in advance!
>
> Best wishes,
> Jonas Van der Paal
> University of Antwerp (Belgium)
>
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> <qm.inp><qmmm.inp>
>
>
>
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