[CP2K:2563] QM/MM with isolated QM box

[Pablo Campomanes]

Hi Shihao,

It seems that you didn't set up explicitly any parameters for your QM simulation box... but it is impossible to say if it could be the origin of your "strange" problem because, as Teo has already pointed out, it is difficult to say something concerning your input without having some more information about the contents of your "include" files.

Regards,

Pablo.
_____________________________________________
Pablo Campomanes
Laboratory of Computational Chemistry and Biochemistry 
BCH 4118 EPF Lausanne


On Feb 17, 2010, at 7:22 PM, shihao wrote:

> 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
> 
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