[CP2K-user] [CP2K:17613] Re: QMMM error message

[Marcella Iannuzzi]

Dear ..
 Most probably you should increase the QMMM cell.
Regards
Marcella

On Tuesday, September 6, 2022 at 12:35:40 AM UTC+2 saja.ma... at gmail.com 
wrote:

> Hello,
> I'm running QMMM MD simulation but got the following error message.
> Can someone help me with this issue?
>
> "
> *A non-periodic calculation has been requested but the system size*
> *exceeds the cell size in at least one of the non-periodic*"
>
> Here is my input file:
>
> &GLOBAL
>   PROJECT METADYN
>   PRINT_LEVEL LOW
>   RUN_TYPE MD
> &END GLOBAL
>
> &FORCE_EVAL
>   METHOD QMMM
>   STRESS_TENSOR ANALYTICAL
>   &DFT
>     CHARGE 0
>     MULTIPLICITY 1
>     &QS
>       METHOD GPW
>     &END QS
>
>     &POISSON
>       PERIODIC XYZ #Direction(s) of PBC for calculating electrostatics
>       PSOLVER PERIODIC #The way to solve Poisson equation
>     &END POISSON
>
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>       &VDW_POTENTIAL
>         POTENTIAL_TYPE PAIR_POTENTIAL
>         &PAIR_POTENTIAL
>           TYPE DFTD3(BJ)
>           PARAMETER_FILE_NAME ./dftd3.dat
>           REFERENCE_FUNCTIONAL PBE
>           CALCULATE_C9_TERM .TRUE.
>           R_CUTOFF [angstrom] 10.0
>         &END PAIR_POTENTIAL
>       &END VDW_POTENTIAL
>     &END XC
>
>     &MGRID
>       COMMENSURATE
>       CUTOFF 300
>       REL_CUTOFF 40
>     &END MGRID
>
>
>     &SCF
>       MAX_SCF 30
>       EPS_SCF 1.0E-6
>       SCF_GUESS ATOMIC
>       &OT
>         MINIMIZER DIIS
>         PRECONDITIONER FULL_SINGLE_INVERSE
>       &END
>       &OUTER_SCF
>         EPS_SCF 1.0E-6
>         MAX_SCF 10
>       &END
>       &PRINT
>         &RESTART OFF
>         &END
>         &RESTART_HISTORY OFF
>         &END
>       &END
>     &END SCF
>
>     BASIS_SET_FILE_NAME BASIS_MOLOPT 
>     POTENTIAL_FILE_NAME GTH_POTENTIALS
>     WFN_RESTART_FILE_NAME WFN-RESTART.wfn
>   &END DFT
>
>
>   &MM
>     &FORCEFIELD
>       PARMTYPE AMBER
>       PARM_FILE_NAME protein_LJ_mod.prmtop
>       &SPLINE
>         EMAX_SPLINE 1.0E8
>         RCUT_NB [angstrom] 10
>       &END SPLINE
>     &END FORCEFIELD
>     &POISSON
>       &EWALD
>         EWALD_TYPE SPME
>         ALPHA .40
>         GMAX 80
>       &END EWALD
>     &END POISSON
>   &END MM
>
>
>   &SUBSYS
>     &CELL
>       ABC [angstrom] 114.2123865514 114.2126337318 114.3616721715 
> <(361)%20672-1715> 
>       ALPHA_BETA_GAMMA 90 90 90
>     &END CELL
>     &TOPOLOGY
>       CONN_FILE_FORMAT AMBER
>       CONN_FILE_NAME protein_LJ_mod.prmtop
>     &END TOPOLOGY
>
>    &KIND C
>     ELEMENT C
>     BASIS_SET DZVP-MOLOPT-GTH
>     POTENTIAL GTH-PBE-q4
>    &END KIND
>    &KIND H
>     ELEMENT H
>     BASIS_SET DZVP-MOLOPT-GTH
>     POTENTIAL GTH-PBE-q1
>    &END KIND
>    &KIND N
>     ELEMENT N
>     BASIS_SET DZVP-MOLOPT-GTH
>     POTENTIAL GTH-PBE-q5
>    &END KIND
>    &KIND O
>     ELEMENT O
>     BASIS_SET DZVP-MOLOPT-GTH
>     POTENTIAL GTH-PBE-q6
>    &END KIND
>    &KIND P
>     ELEMENT P
>     BASIS_SET DZVP-MOLOPT-GTH
>     POTENTIAL GTH-PBE-q5
>    &END KIND
>    &KIND NA+
>     ELEMENT Na
>    &END KIND
>    &KIND Cl-
>     ELEMENT Cl
>    &END KIND
>
>   &END SUBSYS
>
>   &QMMM
>     ECOUPL GAUSS
>     USE_GEEP_LIB 6
>     &CELL
>       ABC 20 20 20
>       ALPHA_BETA_GAMMA 90 90 90
>     &END CELL
>
>     &QM_KIND O
>       MM_INDEX 5630 5627 5621 5595 5596 5205 5206 5346
>     &END QM_KIND
>
>     &QM_KIND C
>       MM_INDEX 5583 5584 5585 5586 5588 5589 5590 5591 5592 5593 5594 5615 
> 5626 5620 5619 5622 5201 5204 5337 5340 5341 5343 5345 5348 5350
>     &END QM_KIND
>
>     &QM_KIND H
>       MM_INDEX 5640 5641 5638 5639 5636 5637 5634 5635 5633 5632 5631 5628 
> 5623 5624 5625 5629 5616 5617 5618 5203 5202 5207 5338 5339 5342 5344 5347 
> 5349 5351
>     &END QM_KIND
>
>     &QM_KIND N
>       MM_INDEX 5587
>     &END QM_KIND
>
>
>
>
>     &LINK
>       MM_INDEX 6582
>       QM_INDEX 6583
>       LINK_TYPE IMOMM
>     &END LINK
>
>     &LINK
>       MM_INDEX 5597
>       QM_INDEX 5593
>       LINK_TYPE IMOMM
>     &END LINK
>
>     &LINK
>       MM_INDEX 5199
>       QM_INDEX 5201
>       LINK_TYPE IMOMM
>     &END LINK
>
>     &LINK
>       MM_INDEX 5335
>       QM_INDEX 5337
>       LINK_TYPE IMOMM
>     &END LINK
>
>   &END QMMM
> &END FORCE_EVAL
>
> &MOTION
>   &MD
>   ENSEMBLE NVT
>   TIMESTEP [fs] 0.5
>   STEPS    2000000  
>   TEMPERATURE 298
>   &THERMOSTAT
>     TYPE NOSE
>     REGION GLOBAL
>     &NOSE
>       TIMECON [fs] 100.
>     &END NOSE
>   &END THERMOSTAT
>   &END MD
>
>
>
>   &FREE_ENERGY
>     METHOD METADYN
>     &METADYN
>       USE_PLUMED .TRUE.
>       PLUMED_INPUT_FILE ./plumed.in
>     &END METADYN
>   &END FREE_ENERGY
>
>    &PRINT
>     &RESTART                                    
>       &EACH                                 
>         MD 100
>       &END
>     &END
>     &RESTART_HISTORY                           
>       &EACH                                     
>         MD 100
>       &END
>     &END
>     &TRAJECTORY                             
>       FORMAT DCD                              
>       &EACH                                     
>         MD 20
>       &END
>     &END
>   &END PRINT
> &END MOTION
>
> &EXT_RESTART
>   RESTART_FILE_NAME NPT-1.restart
>   RESTART_COUNTERS .FALSE.
>   RESTART_THERMOSTAT .FALSE.
> &END
>

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