[CP2K-user] [CP2K:16464] Re: PBC within QM/MM

[Marcella Iannuzzi]

Dear Ludwig,

Yes you are right,  sorry for the confusion. The default for QMMM&CELL is 
periodic none, because the pair lists are constructed according to the 
periodicity of the MM cell. 
The PERIODIC&POISSON sections control the electrostatics interactions (all 
of them). Hence, if you do not want them to be periodic, set them to NONE.

Regards
Marcella

On Monday, January 17, 2022 at 11:32:33 AM UTC+1 Ludwig wrote:

> Dear Marcella,
>
> Thanks a lot for the reply! What confuses me is the fact that *2. 
> /QMMM/CELL/PERIODIC* is None by default, is it not necessary to set it to 
> XYZ for a fully QM/MM periodic calculation? The CELL section is only 
> updating pair lists for the short-ranged real part of Ewald, and also 
> updating coordinates in case they get out of the primary cell? And to 
> neglect all QM interactions with the periodic images (as if the QM region 
> were “isolated”), is it enough to set *3. /DFT/POISSON/PERIODIC* and *5. 
> /QMMM/PERIODIC/POISSON/PERIODIC* equal to None?
>
> Thanks again for your help,
>
> Ludwig
>
> On Friday, January 14, 2022 at 10:23:28 AM UTC+1 Marcella Iannuzzi wrote:
>
>>
>> Dear Ludwig, 
>>
>> Section 1 and 2 control only the periodicity of the coordinates, but not 
>> of the electrostatic interactions. 
>> For a fully periodic QMMM calculation you need PERIODIC XYZ both in CELL 
>> as well as in POISSON, which by the way are the default. 
>> In addition, you might want to specify the section PERIODIC in QMMM, 
>> CP2K_INPUT <https://manual.cp2k.org/trunk/CP2K_INPUT.html> / FORCE_EVAL 
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL.html> / QMMM 
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM.html> / 
>> PERIODIC 
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/QMMM/PERIODIC.html>
>> something like (example taken from regtests)
>>
>>     &PERIODIC
>>
>>      GMAX 0.1
>>
>>       &MULTIPOLE
>>
>>        RCUT 30.0
>>
>>        EWALD_PRECISION 0.000001
>>
>>       &END
>>
>>     &END
>>
>>
>> Regards
>>
>> Marcella
>> On Thursday, January 13, 2022 at 11:00:12 AM UTC+1 Ludwig wrote:
>>
>>> Dear all,
>>>
>>> I have a doubt on how to define periodic boundary conditions (PBC) for a 
>>> QM/MM system (protein with a small QM region and a large MM region that 
>>> includes solvent). As far as I have seen, there are several sections where 
>>> one can define cell information (sections 1-2 beneath) and Poisson solver 
>>> methods for electrostatic interactions (sections 3-5):
>>>
>>> *1. /SUBSYS/CELL/PERIODIC* (default XYZ)*: Specify the directions for 
>>> which periodic boundary conditions (PBC) will be applied. Important notice: 
>>> This applies to the generation of the pair lists as well as to the 
>>> application of the PBCs to positions. See the POISSON section to specify 
>>> the periodicity used for the electrostatics. * 
>>>
>>> *2. /QMMM/CELL/PERIODIC* (default None): *Specify the directions for 
>>> which periodic boundary conditions (PBC) will be applied. Important notice: 
>>> This applies to the generation of the pair lists as well as to the 
>>> application of the PBCs to positions.*
>>>
>>> *3. /DFT/POISSON/PERIODIC* (default XYZ): *Specify the directions in 
>>> which PBC apply. Important notice, this only applies to the electrostatics. 
>>> See the CELL section to specify the periodicity used for e.g. the pair 
>>> lists.*
>>>
>>> *4. /MM/POISSON/PERIODIC* (default XYZ): *Specify the directions in 
>>> which PBC apply. Important notice, this only applies to the electrostatics. 
>>> See the CELL section to specify the periodicity used for e.g. the pair 
>>> lists.*
>>>
>>> *5. /QMMM/PERIODIC/POISSON**/PERIODIC* (default XYZ): *Specify the 
>>> directions in which PBC apply. Important notice, this only applies to the 
>>> electrostatics. See the CELL section to specify the periodicity used for 
>>> e.g. the pair lists.*
>>>
>>> *If I understand this correctly**, in a QM/MM framework section **1** 
>>> can be used to **specify** the periodicity of the large MM **cell** 
>>> that encloses the entire system, and section **2** to define the 
>>> periodicity of the small QM **cell* *that encloses the electron density 
>>> **(using the Blöchl **decoupling scheme** described in Laino2006?).*
>>>
>>> *What is a bit confusing **to** me are sections **3**, **4**, and **5, **when 
>>> section **2** is either None or **Periodic**. **What are these three 
>>> sections controlling exactly? The **electrostatic interactions between 
>>> (3) **QM-QM’, **(4) **MM-MM’,* *and (5) **QM-MM’ / **MM-QM’* *atoms in 
>>> the **primary–periodic’ cells**? **What happens with **3 and 5** if 
>>> section 2 is set to None (*i.e. *system without QM' images)?*
>>>
>>> *Thanks in advance**,*
>>>
>>> *Ludwig*
>>>
>>

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