confusion about QM/MM setup in CP2k

[Sun Tao]

Dear Matt:

I am trying to carry out some simulations with periodic boundary condition. 
However, no matter ab initio MD or QM/MM simulations gave me some 
configurations with atoms moving out of the cell box. Please find the 
attached snapshots for the simulation of water inside carbon nanotube. The 
initial setup is in picture 0.0ps.png with the rectangular simulation box. 
The configuration after 1.2 picoseconds, the atoms are moving out of the 
simulation box. Both the snapshots were taken from the trajectory file 
*-pos-1.xyz file. 

I am also attaching the input files. In FORCE_EVAL/DFT/POISSON section, 
the PERIODIC tag was set to XYZ, and in FORCE_EVAL/SUBSYS/CELL section, 
the PERIODIC tag was not set and the default should also be XYZ. Then I 
don't know why the atoms are moving out of the cell box.

Sorry to bother you again. Thanks very much for your help.

Tao


在 2017年5月26日星期五 UTC-5下午6:07:41，Matt W写道：
>
>
>> 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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