[CP2K-user] [CP2K:20526] problem regarding REFTRAJ calculation

[Chintu Das]

Dear All

I am trying to use REFTRAJ to calculate force and energy from trajectory 
file. 

&GLOBAL
  PROJECT MD
  PRINT_LEVEL LOW
  RUN_TYPE MD
&END GLOBAL

&FORCE_EVAL
  METHOD QMMM
  STRESS_TENSOR ANALYTICAL
  &DFT
    &LS_SCF
      EXTRAPOLATION_ORDER 3
    &END LS_SCF
    BASIS_SET_FILE_NAME  BASIS_MOLOPT
    POTENTIAL_FILE_NAME  POTENTIAL
    &MGRID
      CUTOFF 280
      REL_CUTOFF 40
      NGRIDS 5
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-6
      EXTRAPOLATION_ORDER 3
    &END QS
    &SCF
      SCF_GUESS ATOMIC
      &OT ON
        MINIMIZER DIIS
      &END OT
      EPS_SCF      1.0E-6
      &PRINT
        &RESTART OFF
        &END
      &END
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
      &vdW_POTENTIAL
         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
         &PAIR_POTENTIAL
            TYPE DFTD3(BJ)
            PARAMETER_FILE_NAME dftd3.dat
            REFERENCE_FUNCTIONAL PBE
         &END PAIR_POTENTIAL
      &END vdW_POTENTIAL
    &END XC
  &END DFT
  &MM
    &FORCEFIELD
      PARMTYPE AMBER
      PARM_FILE_NAME System.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] 58.9710000  58.6940000  57.5120000
      ALPHA_BETA_GAMMA 90 90 90
    &END CELL
    &TOPOLOGY
      CONN_FILE_FORMAT AMBER
      CONN_FILE_NAME System.prmtop
      COORD_FILE_FORMAT CRD
      COORD_FILE_NAME System.inpcrd
    &END TOPOLOGY

    &KIND H
      ELEMENT H
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND
    &KIND C
      ELEMENT C
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND O
      ELEMENT O
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND F
      ELEMENT F
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q7
    &END KIND

  &END SUBSYS
  &QMMM
    ECOUPL NONE
    !USE_GEEP_LIB 5
    CENTER EVERY_STEP
    &CELL
      ABC 30 30 30
      ALPHA_BETA_GAMMA 90 90 90
    &END CELL
    &QM_KIND O
      MM_INDEX 64 471 59 46 334 347 468 41 329 352 437 441 451 457 466
    &END QM_KIND
    &QM_KIND H
      MM_INDEX 57 65 60 54 51 53 52 47 39 42 330 327 335 342 339 341 340 
345 353 348 472 473 469 470 434 435 436 439 443 444 445 446 448 450 453 455 
456 459 460 461 463 464 465 467
    &END QM_KIND
    &QM_KIND C
      MM_INDEX 66 63 61 58 55 56 49 50 48 45 43 40 37 38 325 326 336 333 
331 328 337 338 343 346 344 354 351 349 433 438 440 442 447 449 452 454 458 
462
   &END QM_KIND

    &QM_KIND F
      MM_INDEX 62 44 332 350
    &END QM_KIND
    &LINK
      MM_INDEX 67
      QM_INDEX 66
      LINK_TYPE IMOMM
    &END LINK
    &LINK
      MM_INDEX 31
      QM_INDEX 37
      LINK_TYPE IMOMM
    &END LINK
    &LINK
      MM_INDEX 355
      QM_INDEX 354
      LINK_TYPE IMOMM
    &END LINK
    &LINK
      MM_INDEX 319
      QM_INDEX 325
      LINK_TYPE IMOMM
    &END LINK

  &END QMMM

&END FORCE_EVAL

&MOTION
  &MD
    ENSEMBLE REFTRAJ
    &REFTRAJ
      EVAL_ENERGY_FORCES T
      EVAL_FORCES T
      TRAJ_FILE_NAME traj_till3n.xyz
      FIRST_SNAPSHOT 1
      LAST_SNAPSHOT 1993
      STRIDE 1
    &END REFTRAJ

  &END MD

&END MOTION


But its not working with the following error


 *** WARNING in qmmm_util.F:190 :: One or few QM atoms are within the SKIN 
***
 *** of the quantum box. Check your run and you may possibly consider: the 
***
 *** activation of the QMMM WALLS around the QM box, switching ON the     
 ***
 *** centering of the QM box or increase the size of the QM cell. CP2K     
***
 *** CONTINUE but results could be meaningless.                           
 ***

I am not sure why is it not centering the qm part in the given box. Because 
I use the same qm settings to run a MD with level of theory and it works. 
But during reftraj its not centering the qm part and which maybe creating 
the problem. Any suggestion will be really helpful. 

Thank you.

Kind regards
Chintu

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