Non-periodic QM region

QM/MM for Biomolecular Simulation
1

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

2

Hi,

Try to remove them completely from the CP2K input file.

3

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

All the best,
Qinghua

4

Could you share QMMM section in the GROMACS mdp file?

5

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
;

6

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