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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