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

Laino Teodoro teodor... at gmail.com
Thu Feb 18 00:24:52 CET 2010


Hi Shihao,

are you able to reproduce the error with a small system (max 3 QM  
atoms, let's say water, and not more than other 3 MM atoms, let's say  
again water)?
Your input below is useless due to the lack of so many other  
important pieces of input like the INCLUDE files.
To be kind I would say that it's spam.

Regards,
Teo

On 17 Feb 2010, at 19:22, 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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