confusion about QM/MM setup in CP2k

Matt W mattwa... at gmail.com
Sat May 27 01:07:40 CEST 2017


>
>
> Thanks very much for your help! I checked the 2 papers, here is my 
> understanding. The 2005 paper about QM/MM electrostatic coupling does allow 
> MM atoms to be inside the QM box. I guess the QM box setup in CP2K is just 
> to apply the scheme in the 2006 paper to calculate the electrostatic 
> interaction within periodic  boundary condition. I have some more questions:
>
> 1. Does the size of the QM box affect the simulation speed a lot? I could 
> just set up the QM box to be the same as the overall system box, then 
> specify some important part to be treated in QM fasion while other atoms in 
> MM. Is it necessary to set up a smaller QM box?
>
> Depends on the size/density of your system, for various reasons. You might 
pay quite a lot for empty space using CP2K in a small system, but 
negligible for a larger one.

 

> 2. If I set up a smaller QM box, the the box boundary cuts through a 
> covalent bond, do I need to cap the dangling bond with hydrogen atoms as 
> what is usually done for QM/MM?
>
> Yes, you'd need to cap the dangling bonds, entirely as you'd expect.

 

> 3. Inside a QM box, for example there is a covalent bond A-B. Now I set 
> atom A to be treated in QM, while atom B to be treated in MM, does this 
> seem to be a correct way? Further more the covalent bond A-B is actually 
> within a piece of solid, and the solid is kept fixed (does not move).
>
> As long as you have some forcefield that can describe the interaction. 
Again, the boxes are pretty much for electrostatics, what really matters is 
whether there are changes in the bonding of the system.
 

> Thanks again for your help!
>
> Tao
>
> 在 2017年5月25日星期四 UTC-5下午4:25:27,Matt W写道:
>>
>> Hi Tao,
>>
>> The boxes are used essentially for electrostatic calculations. The 
>> interface between the QM and MM atoms is the real region where they 
>> connect, not really anything to do with the cells.
>>
>> You should see a list of relevant references at the end of the output 
>> file - there are two particular to CP2K by Laio and co-workers that you 
>> should try and read.
>>
>> Matt 
>>
>> On Thursday, May 25, 2017 at 6:09:31 PM UTC+1, Sun Tao wrote:
>>>
>>> Dear experts:
>>>
>>> I am confused about some settings of the QMMM portion of CP2K. In the 
>>> section QMMM/CELL we need to set up the QM region. Then in QMMM/QM_KIND 
>>> section, there is a keyword MM_INDEX, for which my understanding is to tell 
>>> the program the index of the MM atoms that would be treated in QM fashion. 
>>>
>>> Here is the question: does CP2K allow MM atoms inside QM regions? Or say 
>>> in the QM region some atoms could be treated in QM and others could still 
>>> be treated in MM? If CP2K does allow this, how do these two different kinds 
>>> of atoms (QM atoms and MM atoms) interact with each other inside the QM 
>>> box? Is there any papers/books I could refer to if this is the case? Before 
>>> I only know that the coupling happens between QM region and MM region and 
>>> the boundary between QM and MM is important to treat. 
>>>
>>> Thanks very much for your help. Look forward to your reply!
>>>
>>> Tao
>>>
>>
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