Dear Ananya:<div>    Have you solved your problem? I am also having the similar issue and looking for help. By the way, maybe you should also turn on the QM box recentering every step? The QM atoms just won't cross the QM box boundary even if you set wall constant to 0 in z direction. Any help from more experienced will be appreciated!</div><div><br></div><div>Thanks</div><div>Ruibin<br><br>On Monday, November 5, 2012 12:53:08 PM UTC-6, Ananya mondal wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Dear cp2k users,
<br>I am trying to setup a  QM/MM simulation of protein in water using CP2K's QM/MM
<br>capabilities. Dimension of the protien is about 25.29 X 25.13 X 22.31 Angstrom.
<br>This protien is solvated in a periodic (XYZ) MM water box of size
<br>40.6411 X 40.6411 X
<br>33.2518 Angstrom. My QM box size is about 26.00 26.00 33.2518 (some
<br>water molecules
<br> are also included in the QM part). I want to apply the periodic
<br>boundary conditions
<br>along the Z direction in my QM part. In the CELL section of the SUBSYS and QMMM
<br>section, I used PERIODIC XYZ and Z, respectively.
<br>
<br>Now, i am little confused with the my input in the poisson section in
<br>the DFT section
<br>and PERIODIC section in the QMMM section, for a periodic (PERIODIC Z)
<br>QMMM calculation. What type of POISSON_SOLVER should i use for this
<br>type of calculation
<br> and what will be the PERIODICITY ?
<br>
<br>I would really appreciate it if people could check whether there are
<br>still other errors in the input.
<br>Thank you in advance for your help.
<br>
<br>Ananya
<br>
<br>
<br>
<br>Here is my input
<br>
<br>@SET FREQ 1
<br>@SET NAME P
<br>@SET PREV 0000
<br>@SET NEXT 0001
<br>@SET qmmm_qm_atoms              'qm_atoms.inp'
<br>@SET qmmm_link_atoms            'link_atoms.inp'
<br>
<br>&GLOBAL
<br>  PROGRAM                       CP2K
<br>  RUN_TYPE                      MD
<br>  PRINT_LEVEL                   LOW
<br>  SAVE_MEM                      T
<br>&END GLOBAL
<br>&FORCE_EVAL
<br>  METHOD QMMM
<br>  &QMMM
<br>    PARALLEL_SCHEME             GRID
<br>    E_COUPL                     GAUSS
<br>    USE_GEEP_LIB                10
<br>    NOCENTER
<br>    &CELL
<br>      ABC                       26.00 26.00 33.2518
<br>      PERIODIC                  Z
<br>    &END CELL
<br>    &PERIODIC                                          #???
<br>      GMAX                      0.5                      #???
<br>      &MULTIPOLE                                     #???
<br>        EWALD_PRECISION         1.0E-6      #???
<br>        RCUT                    13                       #???
<br>      &END
<br>    &WALLS
<br>      WALL_SKIN                 4.0 4.0 0.0      #???
<br>      TYPE                      QUADRATIC       #???
<br>      K                         0.002
<br>    &END WALLS
<br>@INCLUDE ${qm_atoms.inp}
<br>@INCLUDE ${link_atoms.inp}
<br>    &MM_KIND H
<br>      RADIUS                    .32
<br>    &END MM_KIND
<br>    &MM_KIND C
<br>      RADIUS                    .77
<br>    &END MM_KIND
<br>    &MM_KIND N
<br>      RADIUS                    .75
<br>    &END MM_KIND
<br>    &MM_KIND O
<br>      RADIUS                    .73
<br>    &END MM_KIND
<br>  &END QMMM
<br>
<br>  &DFT
<br>    CHARGE                      4
<br>    BASIS_SET_FILE_NAME            ./GTH_BASIS_SETS
<br>    POTENTIAL_FILE_NAME            ./GTH_POTENTIALS
<br>#    WFN_RESTART_FILE_NAME          ./${NAME}_${PREV}.RESTART
<br>    &MGRID
<br>      CUTOFF                    300
<br>      COMMENSURATE
<br>      &RS_GRID
<br>        DISTRIBUTION_TYPE       DISTRIBUTED
<br>      &END RS_GRID
<br>    &END MGRID
<br>    &QS
<br>      METHOD                    GPW
<br>      EPS_DEFAULT               1.0E-12
<br>      WF_INTERPOLATION          ASPC
<br>      EXTRAPOLATION_ORDER       4
<br>    &END QS
<br>    &SCF
<br>      SCF_GUESS                 RESTART
<br>       MAX_SCF                  40
<br>       EPS_SCF                  5.0e-7
<br>      &OT ON
<br>        PRECONDITIONER          FULL_KINETIC
<br>        MINIMIZER               DIIS
<br>        N_DIIS                  7
<br>      &END OT
<br>      &OUTER_SCF
<br>        MAX_SCF                 10
<br>        EPS_SCF                 5.0e-7
<br>      &END OUTER_SCF
<br>    &END SCF
<br>    &XC
<br>      &XC_FUNCTIONAL            BLYP
<br>      &END XC_FUNCTIONAL
<br>      &vdW_POTENTIAL
<br>         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
<br>         &PAIR_POTENTIAL
<br>            TYPE DFTD3
<br>            PARAMETER_FILE_NAME ./dftd3.dat
<br>            REFERENCE_FUNCTIONAL BLYP
<br>            LONG_RANGE_CORRECTION .TRUE.
<br>            D3_SCALING 1.0      1.094   1.682
<br>            R_CUTOFF 12.
<br>         &END PAIR_POTENTIAL
<br>      &END vdW_POTENTIAL
<br>    &END XC
<br>    &POISSON                                            #???
<br>      PERIODIC                  Z                        #???
<br>      POISSON_SOLVER            PERIODIC  #???
<br>    &END POISSON
<br>  &END DFT
<br>  &MM
<br>    &FORCEFIELD
<br>        PARMTYPE                CHM
<br>        PARM_FILE_NAME          par_all27_prot_lipid.prm
<br>    &END FORCEFIELD
<br>    &POISSON
<br>      &EWALD
<br>        EWALD_TYPE              spme
<br>        ALPHA                   0.44
<br>        GMAX                    96
<br>        O_SPLINE                6
<br>      &END EWALD
<br>    &END POISSON
<br>  &END MM
<br>  &SUBSYS
<br>    &CELL
<br>      ABC                       40.6411 40.6411 33.2518
<br>      PERIODIC                  XYZ
<br>    &END CELL
<br>    &TOPOLOGY
<br>      COORD_FILE_NAME           p.pdb
<br>      COORD_FILE_FORMAT         PDB
<br>      CONN_FILE_NAME            p.psf
<br>      CONN_FILE_FORMAT          UPSF
<br>    &END TOPOLOGY
<br>
<br>    &KIND H
<br>      BASIS_SET                 TZV2P-GTH
<br>      POTENTIAL                 GTH-BLYP-q1
<br>    &END KIND
<br>    &KIND O
<br>      BASIS_SET                 TZV2P-GTH
<br>      POTENTIAL                 GTH-BLYP-q6
<br>    &END KIND
<br>    &KIND N
<br>      BASIS_SET                 TZV2P-GTH
<br>      POTENTIAL                 GTH-BLYP-q5
<br>    &END KIND
<br>    &KIND C
<br>      BASIS_SET                 TZV2P-GTH
<br>      POTENTIAL                 GTH-BLYP-q4
<br>    &END KIND
<br>  &END SUBSYS
<br>
<br>&END FORCE_EVAL
<br>
<br>
<br>&MOTION
<br>  &MD
<br>    TIMESTEP                    0.25
<br>    STEPS                       10
<br>    ENSEMBLE                    NVT
<br>    TEMPERATURE                 300
<br>    &THERMOSTAT
<br>      TYPE                         CSVR
<br>       &CSVR
<br>         TIMECON                   20
<br>       &END CSVR
<br>      &DEFINE_REGION
<br>        MM_SUBSYS               MOLECULAR
<br>      &END DEFINE_REGION
<br>      &DEFINE_REGION
<br>        QM_SUBSYS               ATOMIC
<br>      &END DEFINE_REGION
<br>    &END THERMOSTAT
<br>  &END MD
<br>  &PRINT
<br>    &TRAJECTORY                    SILENT
<br>      &EACH
<br>        MD                         ${FREQ}
<br>      &END EACH
<br>      FILENAME                     =${NAME}_${NEXT}.dcd
<br>      FORMAT                       DCD
<br>    &END TRAJECTORY
<br>    &RESTART                       SILENT
<br>      &EACH
<br>        MD                         ${FREQ}
<br>      &END EACH
<br>      FILENAME                     =${NAME}_${NEXT}.restart
<br>    &END RESTART
<br>  &END PRINT
<br>&END MOTION
<br></blockquote></div>