Coordinates of QM/MM link atoms

Vladimir Mironov nev... at gmail.com
Mon Jun 13 11:15:42 UTC 2011


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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