[CP2K-user] [CP2K:16516] Re: PBC within QM/MM
Ludwig
lraichar at gmail.com
Thu Jan 27 15:27:18 UTC 2022
Dear Marcella,
Thanks a lot for all your clarifications, it is really helpful! I am not
sure to see what is the practical use of the QMMM*/*CELL/PERIODIC command. If
the QM and MM boxes are equal, then this command is just the same as the
one in SUBSYS, right? And if the QM cell is smaller than the MM one, activating
this option would not include in the pair lists short-range interactions
that in reality are not within the cutoff?
I made a quick scheme of the different options, the question above would be
represented by setup 2 compared to 1. I would not expect large differences
between the two setups, but still to me it makes more sense setup 1, which
is the one by default if one explicitly writes the POISSON section in &QMMM
(I suppose that missing this section without deactivating the one at &DFT
would lead to fictitious periodic QM images within the MM cell).
Thanks again,
Ludwig
On Monday, January 17, 2022 at 2:16:52 PM UTC+1 Marcella Iannuzzi wrote:
>
> 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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