[CP2K:7704] Setting up QMMM simulation (much slower than QM part only)

Teodoro Laino teodor... at gmail.com
Thu Apr 21 16:44:52 CEST 2016


it’s not that simple though..
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.
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.




> On 21 Apr 2016, at 13:24, jonas.va... at uantwerpen.be wrote:
> 
> 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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