# Non-periodic QM region

**URL:** <https://ask.bioexcel.eu/t/non-periodic-qm-region/4080>\
**Category:** QM/MM for Biomolecular Simulation\
**Created:** [January 20, 2023, 2:48pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080 "2023-01-20T14:48:28Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Qinghua](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\
**Post date:** [January 20, 2023, 2:48pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/1 "2023-01-20T14:48:28Z")

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Hello,

In my QM/MM simulation with Gromacs 2022.3 / CP2K 2023.1, I used non-periodic QM region in the CP2K input file, as I commented out the following lines in the QMMM block:

! &PERIODIC  
! GMAX 1.0E+00  
! &MULTIPOLE ON  
! RCUT 1.0E+01  
! EWALD\_PRECISION 1.0E-06  
! &END  
! &END PERIODIC

However, during the simulation, I found that those lines are still active in the newly generated CP2K input files, somehow, Gromacs removed the sign “!” in the simulation, no matter what:

```
&PERIODIC
  GMAX 1.0E+00
  &MULTIPOLE ON
     RCUT 1.0E+01
     EWALD_PRECISION 1.0E-06
  &END
&END PERIODIC

```

As I already turned the QM box as non-periodic in the QMMM block:  
&CELL  
A 16.000 0.000 0.000  
B 0.000 20.000 0.000  
C 0.000 0.000 16.000  
PERIODIC NONE  
&END CELL

With this combination, I am not sure how the calculations are done. Could someone give me some comments on it? Thanks a lot!

All the best,  
Qinghua

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<div class="post-metadata">

**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\
**Post date:** [January 24, 2023, 3:11pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/2 "2023-01-24T15:11:14Z")

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Hi,

Try to remove them completely from the CP2K input file.

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<div class="post-metadata">

**Author:** ![Qinghua](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\
**Post date:** [January 24, 2023, 3:24pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/3 "2023-01-24T15:24:39Z")

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Thanks!  
Actually, I tried to remove them completely, and this block was then added during the simulation.

All the best,  
Qinghua

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<div class="post-metadata">

**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\
**Post date:** [January 24, 2023, 4:03pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/4 "2023-01-24T16:03:54Z")

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Could you share QMMM section in the GROMACS mdp file?

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<div class="post-metadata">

**Author:** ![Qinghua](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\
**Post date:** [January 24, 2023, 5:12pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/5 "2023-01-24T17:12:23Z")

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Thanks!  
Here is my mdp input for the QM/MM calculation:  
; QMMM  
qmmm-cp2k-active = true  
qmmm-cp2k-qmgroup = QMatoms  
qmmm-cp2k-qmmethod = INPUT  
qmmm-cp2k-qmcharge = 0  
qmmm-cp2k-qmmultiplicity = 1  
;

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<div class="post-metadata">

**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\
**Post date:** [January 24, 2023, 5:56pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080/6 "2023-01-24T17:56:35Z")

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check if you are using correct input file in the `grompp` `-qmi` option