confusion about QM/MM setup in CP2k

Matt W mattwa... at gmail.com
Thu Jul 13 17:42:56 CEST 2017


Hi,

there is no outside a periodic box; if you leave one side you come back in 
the other. In VMD or most visualisers you can wrap atoms back into the box.

Matt

On Thursday, July 13, 2017 at 5:22:13 PM UTC+2, Sun Tao wrote:
>
> 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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