[CP2K:3292] Coordinates of QM/MM link atoms

Teodoro Laino teodor... at gmail.com
Mon Jun 13 13:17:27 CEST 2011


Vladimir,

the capping atoms are placed according the parameters provided in the &LINK section.
Wrong parameters produce wrong coordinates.
Triple check your input file.

Teo

On Jun 13, 2011, at 1:15 PM, Vladimir Mironov wrote:

> Hello,
> 
> I am a newbie in cp2k. I have made an MD simulation of protein using
> QM/MM approach. Looking at the QM coordinates in the output file I've
> found that capping hydrogens have the same coordinates as respective
> atoms in the MM subsystem. I'm confused that some of C-H bonds of QM
> subsystem has lengths close or equal to the C-C bond. Shouldn't it
> introduce artifacts into the wavefunction or this behavior is normal?
> Or maybe it can be fixed by some cp2k parameters?
> 
> Thank you in advance for your help.
> 
> Parameters of MD run:
> 
> &GLOBAL
>   PREFERRED_FFT_LIBRARY  FFTMKL
>   EXTENDED_FFT_LENGTHS  T
>   PRINT_LEVEL  MEDIUM
>   PROJECT_NAME 2A50_hsd_flip_ion_md2_nocen_test3
>   RUN_TYPE  MD
> &END GLOBAL
> &MOTION
>   &MD
>     ENSEMBLE  NVT
>     STEPS           40000
>     TIMESTEP     9.9999999999999978E-01
>     STEP_START_VAL            1140
>     TIME_START_VAL     2.1140000000009364E+04
>     ECONS_START_VAL    -6.0233667442417504E+02
>     TEMPERATURE     3.0000000000000000E+02
>     &THERMOSTAT
>       TYPE  NOSE
>       &NOSE
>         &COORD
>               1.5993213746259970E-02   -6.6691198953364861E+00
> 7.7034168880466041E+00
>         &END COORD
>         &VELOCITY
>               1.4118686422651567E-08    9.0362681748106454E-06
> -2.3142327990472863E-06
>         &END VELOCITY
>         &MASS
>               1.3237458199353259E+11    1.6237299232570694E+06
> 1.6237299232570694E+06
>         &END MASS
>         &FORCE
>               2.0303233981634771E-13   -5.6884916460484813E-10
> -5.0344599597395492E-10
>         &END FORCE
>       &END NOSE
>     &END THERMOSTAT
>     &AVERAGES  T
> ...
>     &END AVERAGES
>   &END MD
>   &PRINT
>     &TRAJECTORY  SILENT
>       FORMAT  DCD
>       &EACH
>         MD              10
>       &END EACH
>     &END TRAJECTORY
>     &RESTART_HISTORY  SILENT
>       &EACH
>         MD             500
>       &END EACH
>     &END RESTART_HISTORY
>   &END PRINT
> &END MOTION
> &FORCE_EVAL
>   METHOD  QMMM
>   &DFT
>     BASIS_SET_FILE_NAME ../GTH_BASIS_SETS
>     POTENTIAL_FILE_NAME ../POTENTIAL
>     CHARGE              -1
>     &SCF
>       MAX_ITER_LUMO           12000
>       MAX_SCF             300
>       EPS_SCF     4.9999999999999998E-07
>       SCF_GUESS  RESTART
>       &OT  T
>         MINIMIZER  DIIS
>         STEPSIZE     2.0000000000000001E-01
>         PRECONDITIONER  FULL_ALL
>       &END OT
>       &OUTER_SCF  T
>         EPS_SCF     4.9999999999999998E-07
>         MAX_SCF              20
>       &END OUTER_SCF
>     &END SCF
>     &QS
>       EXTRAPOLATION  PS
>       EXTRAPOLATION_ORDER               3
>       METHOD  GPW
>     &END QS
>     &MGRID
>       CUTOFF     2.8000000000000000E+02
>       COMMENSURATE  T
>       REL_CUTOFF     5.0000000000000000E+01
>     &END MGRID
>     &XC
>       DENSITY_CUTOFF     1.0000000000000000E-10
>       GRADIENT_CUTOFF     1.0000000000000000E-10
>       TAU_CUTOFF     1.0000000000000000E-10
>       &XC_GRID
>         XC_DERIV  SPLINE3
>       &END XC_GRID
>       &XC_FUNCTIONAL  NO_SHORTCUT
>         &BECKE88  T
>         &END BECKE88
>         &LYP  T
>         &END LYP
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>   &MM
>     &FORCEFIELD
>       PARMTYPE  CHM
>       PARM_FILE_NAME ./par_all27_prot_lipid.inp
>       VDW_SCALE14     1.0000000000000000E+00
>       EI_SCALE14     1.0000000000000000E+00
>       IGNORE_MISSING_CRITICAL_PARAMS  T
>       &SPLINE
>         RCUT_NB     1.0000000000000009E+01
>         EMAX_SPLINE     1.0000000000000000E+00
>       &END SPLINE
>     &END FORCEFIELD
>     &NEIGHBOR_LISTS
>       GEO_CHECK  F
>     &END NEIGHBOR_LISTS
>     &POISSON
>       &EWALD
>         EWALD_TYPE  SPME
>         GMAX              64             72             64
>       &END EWALD
>     &END POISSON
>   &END MM
>   &QMMM
>     E_COUPL  GAUSS
>     USE_GEEP_LIB              15
>     NOCENTER  T
>     NOCENTER0  F
>     INITIAL_TRANSLATION_VECTOR    -2.5358636769892726E+00
> -2.7340044931383645E+00   -6.5428856961483941E+00
>     &QM_KIND C
>       MM_INDEX  ...
>     &END QM_KIND
>     &QM_KIND H
>       MM_INDEX   ...
>     &END QM_KIND
>     &QM_KIND N
>       MM_INDEX   ...
>     &END QM_KIND
>     &QM_KIND O
>       MM_INDEX  ...
>     &END QM_KIND
>     &CELL
>       ABC     2.6000000000000000E+01    2.2000000000000000E+01
> 2.2000000000000000E+01
>       PERIODIC  NONE
>     &END CELL
>     &PERIODIC
>       GMAX     1.0000000000000000E+00
>       &MULTIPOLE
>         RCUT     5.0000000000000044E+00
>       &END MULTIPOLE
>     &END PERIODIC
>     &LINK
>       QM_INDEX             989
>       QM_KIND H
>       MM_INDEX             992
>     &END LINK
>     &LINK
>       QM_INDEX            1007
>       QM_KIND H
>       MM_INDEX            1009
>     &END LINK
>     &LINK
>       QM_INDEX            1007
>       QM_KIND H
>       MM_INDEX            1014
>     &END LINK
>     &LINK
>       QM_INDEX            1029
>       QM_KIND H
>       MM_INDEX            1026
>     &END LINK
>     &LINK
>       QM_INDEX            1443
>       QM_KIND H
>       MM_INDEX            1440
>     &END LINK
>     &LINK
>       QM_INDEX            2233
>       QM_KIND H
>       MM_INDEX            2230
>     &END LINK
>     &LINK
>       QM_INDEX            2434
>       QM_KIND H
>       MM_INDEX            2432
>     &END LINK
>     &LINK
>       QM_INDEX            3023
>       QM_KIND H
>       MM_INDEX            3020
>     &END LINK
>     &LINK
>       QM_INDEX            3047
>       QM_KIND H
>       MM_INDEX            3045
>     &END LINK
>     &LINK
>       QM_INDEX            3358
>       QM_KIND H
>       MM_INDEX            3369
>     &END LINK
>     &WALLS
>       TYPE  REFLECTIVE
>     &END WALLS
>   &END QMMM
>   &SUBSYS
>     &CELL
>       A     5.9976500000000001E+01    0.0000000000000000E+00
> 0.0000000000000000E+00
>       B     0.0000000000000000E+00    7.0373999999999995E+01
> 0.0000000000000000E+00
>       C     0.0000000000000000E+00    0.0000000000000000E+00
> 6.1826800000000034E+01
>       MULTIPLE_UNIT_CELL               1              1
> 1
>     &END CELL
>     &COORD
> ...
>     &END COORD
>     &VELOCITY
> ...
>     &END VELOCITY
>     &KIND C
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q4
>       &BASIS
> ...
>       &END BASIS
>       &POTENTIAL
> ...
>       &END POTENTIAL
>     &END KIND
>     &KIND O
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q6
>       &BASIS
> ...
>       &END BASIS
>       &POTENTIAL
> ...
>       &END POTENTIAL
>     &END KIND
>     &KIND N
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q5
>       &BASIS
> ...
>       &END BASIS
>       &POTENTIAL
> ...
>       &END POTENTIAL
>     &END KIND
>     &KIND H
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q1
>       &BASIS
> ...
>       &END BASIS
>       &POTENTIAL
> ...
>       &END POTENTIAL
>     &END KIND
>     &TOPOLOGY
>       COORD_FILE_NAME ./2A50_A2_hsd_flip_ion_eq_end.pdb
>       COORD_FILE_FORMAT  PDB
>       NUMBER_OF_ATOMS           27176
>       CONN_FILE_NAME ./2A50_A2_hsd_flip_ion.psf
>       CONN_FILE_FORMAT  PSF
>       MULTIPLE_UNIT_CELL               1              1
> 1
>     &END TOPOLOGY
>   &END SUBSYS
> &END FORCE_EVAL
> 
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