[CP2K-user] [CP2K:16454] Re: PBC within QM/MM

[Marcella Iannuzzi]

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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