[CP2K-user] [CP2K:16451] PBC within QM/MM

[Ludwig]

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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