QM/MM with isolated QM box

[shihao]

Hi there,

I've been running some QM/MM simulations with periodic MM and isolated
QM box (the QM box is in the center of the cell). However, some
molecules tend to orient in a strange way (eg. parallel to XY, XZ or
YZ plane). I'm pretty sure that this is not because of interactions
from MM region.  I've done all kinds of tests (different QM box sizes,
wall widths, etc.) but still couldn't figure out where the problem is.
Has anyone got experiences with this problem? Any clues will be
greatly appreciated.

Also, is it necessary to specify PERIODIC section in QMMM? I've tried
it but didn't succeed.

Regards,
Shihao

P.S. Here's the input file.  I didn't provide the additional files
(potential, pdb, psf, etc.),  but please let me know if they are
needed and I will simplify them and upload them as well.
&GLOBAL
  PROGRAM_NAME                 CP2K
  PROJECT_NAME                 project
  RUN_TYPE                     MD
  SEED                         1000
  PREFERRED_FFT_LIBRARY        FFTW
  PRINT_LEVEL                  LOW
  SAVE_MEM
&END GLOBAL

&FORCE_EVAL
  METHOD QMMM

  &DFT
    BASIS_SET_FILE_NAME        ./GTH_BASIS_SETS
    POTENTIAL_FILE_NAME        ./POTENTIAL
    CHARGE                     1
    MULTIPLICITY               1
    UNRESTRICTED_KOHN_SHAM     F

    &SCF
      SCF_GUESS                ATOMIC
      EPS_SCF                  1.0E-6
      MAX_SCF                  50
      &OUTER_SCF
        MAX_SCF                10
      &END OUTER_SCF
      &OT
        PRECONDITIONER         FULL_SINGLE_INVERSE
        MINIMIZER              DIIS
        N_DIIS                 7
      &END OT
      &PRINT
        &RESTART
          &EACH
            MD                 20
          &END EACH
        &END RESTART
        &RESTART_HISTORY       OFF
        &END RESTART_HISTORY
      &END PRINT
    &END SCF

    &QS
      METHOD                   GPW
      EPS_DEFAULT              1.0E-12
      EXTRAPOLATION            ASPC
    &END QS
    &MGRID
      COMMENSURATE
      CUTOFF                   280
    &END MGRID
    &POISSON
      POISSON_SOLVER           MT
      PERIODIC                 NONE
    &END POISSON

    &XC
      &XC_FUNCTIONAL           BLYP
      &END XC_FUNCTIONAL
      &XC_GRID
        XC_SMOOTH_RHO          NN10
        XC_DERIV               SPLINE2_SMOOTH
      &END XC_GRID
    &END XC

    &PRINT
      &E_DENSITY_CUBE
        &EACH
          MD                   20
        &END EACH
      &END E_DENSITY_CUBE
    &END PRINT
  &END DFT

  &MM
    &FORCEFIELD
      PARMTYPE                 CHM
      PARM_FILE_NAME           ./par_all27_prot_lipid_amm.prm
      &SPLINE
        RCUT_NB                12.0
      &END SPLINE
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE             SPME
        ALPHA                  0.35
        GMAX                   80 80 80
        O_SPLINE               6
      &END EWALD
    &END POISSON
  &END MM

  &QMMM
    USE_GEEP_LIB               7
    E_COUPL                    GAUSS

    @INCLUDE run_001_cp2k.inp

    @INCLUDE mm_kinds

    &WALLS
      TYPE                     REFLECTIVE
      WALL_SKIN                0.5
    &END WALLS

    &PERIODIC
      GMAX 0.1
      &MULTIPOLE
       RCUT 30.0
       EWALD_PRECISION 0.000001
      &END
    &END

    &PRINT
      &PROGRAM_RUN_INFO        SILENT
      &END PROGRAM_RUN_INFO
      &PERIODIC_INFO           SILENT
      &END PERIODIC_INFO
      &QMMM_LINK_INFO          SILENT
      &END QMMM_LINK_INFO
    &END PRINT
  &END QMMM

  &SUBSYS
    &CELL
      ABC                      92.3237 77.4554 91.24
      PERIODIC                 XYZ
    &END CELL
    &TOPOLOGY
      CONNECTIVITY             UPSF
      CONN_FILE_NAME           ./build.xplor_psf
      COORDINATE               PDB
      COORD_FILE_NAME          ./run_001_cp2k.pdb
      PARA_RES                 T
    &END TOPOLOGY

    ########################################  Basis sets and
pseudopotentials
    &KIND H
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-BLYP-q1
    &END KIND
    &KIND C
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-BLYP-q4
    &END KIND
    &KIND N
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-BLYP-q5
    &END KIND
    &KIND O
      BASIS_SET TZV2P-GTH
      POTENTIAL GTH-BLYP-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL

&MOTION
  &MD
    ENSEMBLE                   LANGEVIN
    STEPS                      2000
    TIMESTEP                   0.50
    TEMPERATURE                298.15
    &LANGEVIN
      GAMMA 0.004
    &END
    &PRINT
      &ENERGY
        &EACH
          MD                   20
        &END EACH
      &END ENERGY
    &END PRINT
  &END MD

  &PRINT
    &RESTART
      &EACH
        MD                     20
      &END EACH
    &END RESTART
    &RESTART_HISTORY           OFF
    &END RESTART_HISTORY

    &TRAJECTORY                SILENT
      FORMAT                   DCD
      &EACH
        MD                     20
      &END EACH
    &END TRAJECTORY
    &VELOCITIES                OFF
    &END VELOCITIES
    &FORCES                    OFF
    &END FORCES
  &END PRINT

  &CONSTRAINT
    &HBONDS
      EXCLUDE_QM               T
    &END HBONDS
    SHAKE_TOLERANCE            1.0E-9
    &LAGRANGE_MULTIPLIERS ON
      COMMON_ITERATION_LEVELS 3
    &END LAGRANGE_MULTIPLIERS
  &END CONSTRAINT
&END MOTION