periodic qmmm calculations

[Ananya Mondal]

Dear cp2k users,
I am trying to setup a  QM/MM simulation of protein in water using CP2K's QM/MM
capabilities. Dimension of the protien is about 25.29 X 25.13 X 22.31 Angstrom.
This protien is solvated in a periodic (XYZ) MM water box of size
40.6411 X 40.6411 X
33.2518 Angstrom. My QM box size is about 26.00 26.00 33.2518 (some
water molecules
 are also included in the QM part). I want to apply the periodic
boundary conditions
along the Z direction in my QM part. In the CELL section of the SUBSYS and QMMM
section, I used PERIODIC XYZ and Z, respectively.

Now, i am little confused with the my input in the poisson section in
the DFT section
and PERIODIC section in the QMMM section, for a periodic (PERIODIC Z)
QMMM calculation. What type of POISSON_SOLVER should i use for this
type of calculation
 and what will be the PERIODICITY ?

I would really appreciate it if people could check whether there are
still other errors in the input.
Thank you in advance for your help.

Ananya



Here is my input

@SET FREQ 1
@SET NAME P
@SET PREV 0000
@SET NEXT 0001
@SET qmmm_qm_atoms              'qm_atoms.inp'
@SET qmmm_link_atoms            'link_atoms.inp'

&GLOBAL
  PROGRAM                       CP2K
  RUN_TYPE                      MD
  PRINT_LEVEL                   LOW
  SAVE_MEM                      T
&END GLOBAL
&FORCE_EVAL
  METHOD QMMM
  &QMMM
    PARALLEL_SCHEME             GRID
    E_COUPL                     GAUSS
    USE_GEEP_LIB                10
    NOCENTER
    &CELL
      ABC                       26.00 26.00 33.2518
      PERIODIC                  Z
    &END CELL
    &PERIODIC                                          #???
      GMAX                      0.5                      #???
      &MULTIPOLE                                     #???
        EWALD_PRECISION         1.0E-6      #???
        RCUT                    13                       #???
      &END
    &WALLS
      WALL_SKIN                 4.0 4.0 0.0      #???
      TYPE                      QUADRATIC       #???
      K                         0.002
    &END WALLS
@INCLUDE ${qm_atoms.inp}
@INCLUDE ${link_atoms.inp}
    &MM_KIND H
      RADIUS                    .32
    &END MM_KIND
    &MM_KIND C
      RADIUS                    .77
    &END MM_KIND
    &MM_KIND N
      RADIUS                    .75
    &END MM_KIND
    &MM_KIND O
      RADIUS                    .73
    &END MM_KIND
  &END QMMM

  &DFT
    CHARGE                      4
    BASIS_SET_FILE_NAME            ./GTH_BASIS_SETS
    POTENTIAL_FILE_NAME            ./GTH_POTENTIALS
#    WFN_RESTART_FILE_NAME          ./${NAME}_${PREV}.RESTART
    &MGRID
      CUTOFF                    300
      COMMENSURATE
      &RS_GRID
        DISTRIBUTION_TYPE       DISTRIBUTED
      &END RS_GRID
    &END MGRID
    &QS
      METHOD                    GPW
      EPS_DEFAULT               1.0E-12
      WF_INTERPOLATION          ASPC
      EXTRAPOLATION_ORDER       4
    &END QS
    &SCF
      SCF_GUESS                 RESTART
       MAX_SCF                  40
       EPS_SCF                  5.0e-7
      &OT ON
        PRECONDITIONER          FULL_KINETIC
        MINIMIZER               DIIS
        N_DIIS                  7
      &END OT
      &OUTER_SCF
        MAX_SCF                 10
        EPS_SCF                 5.0e-7
      &END OUTER_SCF
    &END SCF
    &XC
      &XC_FUNCTIONAL            BLYP
      &END XC_FUNCTIONAL
      &vdW_POTENTIAL
         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
         &PAIR_POTENTIAL
            TYPE DFTD3
            PARAMETER_FILE_NAME ./dftd3.dat
            REFERENCE_FUNCTIONAL BLYP
            LONG_RANGE_CORRECTION .TRUE.
            D3_SCALING 1.0      1.094   1.682
            R_CUTOFF 12.
         &END PAIR_POTENTIAL
      &END vdW_POTENTIAL
    &END XC
    &POISSON                                            #???
      PERIODIC                  Z                        #???
      POISSON_SOLVER            PERIODIC  #???
    &END POISSON
  &END DFT
  &MM
    &FORCEFIELD
        PARMTYPE                CHM
        PARM_FILE_NAME          par_all27_prot_lipid.prm
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE              spme
        ALPHA                   0.44
        GMAX                    96
        O_SPLINE                6
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
    &CELL
      ABC                       40.6411 40.6411 33.2518
      PERIODIC                  XYZ
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME           p.pdb
      COORD_FILE_FORMAT         PDB
      CONN_FILE_NAME            p.psf
      CONN_FILE_FORMAT          UPSF
    &END TOPOLOGY

    &KIND H
      BASIS_SET                 TZV2P-GTH
      POTENTIAL                 GTH-BLYP-q1
    &END KIND
    &KIND O
      BASIS_SET                 TZV2P-GTH
      POTENTIAL                 GTH-BLYP-q6
    &END KIND
    &KIND N
      BASIS_SET                 TZV2P-GTH
      POTENTIAL                 GTH-BLYP-q5
    &END KIND
    &KIND C
      BASIS_SET                 TZV2P-GTH
      POTENTIAL                 GTH-BLYP-q4
    &END KIND
  &END SUBSYS

&END FORCE_EVAL


&MOTION
  &MD
    TIMESTEP                    0.25
    STEPS                       10
    ENSEMBLE                    NVT
    TEMPERATURE                 300
    &THERMOSTAT
      TYPE                         CSVR
       &CSVR
         TIMECON                   20
       &END CSVR
      &DEFINE_REGION
        MM_SUBSYS               MOLECULAR
      &END DEFINE_REGION
      &DEFINE_REGION
        QM_SUBSYS               ATOMIC
      &END DEFINE_REGION
    &END THERMOSTAT
  &END MD
  &PRINT
    &TRAJECTORY                    SILENT
      &EACH
        MD                         ${FREQ}
      &END EACH
      FILENAME                     =${NAME}_${NEXT}.dcd
      FORMAT                       DCD
    &END TRAJECTORY
    &RESTART                       SILENT
      &EACH
        MD                         ${FREQ}
      &END EACH
      FILENAME                     =${NAME}_${NEXT}.restart
    &END RESTART
  &END PRINT
&END MOTION