confusion about QM/MM setup in CP2k

Sun Tao taosun... at gmail.com
Fri May 26 04:48:25 CEST 2017


Dear Matt:

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?

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?

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).

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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