periodic qmmm calculations
Ruibin
ruibin... at gmail.com
Fri Nov 16 00:03:19 UTC 2012
Dear Ananya:
Have you solved your problem? I am also having the similar issue and
looking for help. By the way, maybe you should also turn on the QM box
recentering every step? The QM atoms just won't cross the QM box boundary
even if you set wall constant to 0 in z direction. Any help from more
experienced will be appreciated!
Thanks
Ruibin
On Monday, November 5, 2012 12:53:08 PM UTC-6, Ananya mondal wrote:
>
> Dear cp2k users,
> I am trying to setup a QM/MM simulation of protein in water using CP2K's
> QM/MM
> capabilities. Dimension of the protien is about 25.29 X 25.13 X 22.31
> Angstrom.
> This protien is solvated in a periodic (XYZ) MM water box of size
> 40.6411 X 40.6411 X
> 33.2518 Angstrom. My QM box size is about 26.00 26.00 33.2518 (some
> water molecules
> are also included in the QM part). I want to apply the periodic
> boundary conditions
> along the Z direction in my QM part. In the CELL section of the SUBSYS and
> QMMM
> section, I used PERIODIC XYZ and Z, respectively.
>
> Now, i am little confused with the my input in the poisson section in
> the DFT section
> and PERIODIC section in the QMMM section, for a periodic (PERIODIC Z)
> QMMM calculation. What type of POISSON_SOLVER should i use for this
> type of calculation
> and what will be the PERIODICITY ?
>
> I would really appreciate it if people could check whether there are
> still other errors in the input.
> Thank you in advance for your help.
>
> Ananya
>
>
>
> Here is my input
>
> @SET FREQ 1
> @SET NAME P
> @SET PREV 0000
> @SET NEXT 0001
> @SET qmmm_qm_atoms 'qm_atoms.inp'
> @SET qmmm_link_atoms 'link_atoms.inp'
>
> &GLOBAL
> PROGRAM CP2K
> RUN_TYPE MD
> PRINT_LEVEL LOW
> SAVE_MEM T
> &END GLOBAL
> &FORCE_EVAL
> METHOD QMMM
> &QMMM
> PARALLEL_SCHEME GRID
> E_COUPL GAUSS
> USE_GEEP_LIB 10
> NOCENTER
> &CELL
> ABC 26.00 26.00 33.2518
> PERIODIC Z
> &END CELL
> &PERIODIC #???
> GMAX 0.5 #???
> &MULTIPOLE #???
> EWALD_PRECISION 1.0E-6 #???
> RCUT 13 #???
> &END
> &WALLS
> WALL_SKIN 4.0 4.0 0.0 #???
> TYPE QUADRATIC #???
> K 0.002
> &END WALLS
> @INCLUDE ${qm_atoms.inp}
> @INCLUDE ${link_atoms.inp}
> &MM_KIND H
> RADIUS .32
> &END MM_KIND
> &MM_KIND C
> RADIUS .77
> &END MM_KIND
> &MM_KIND N
> RADIUS .75
> &END MM_KIND
> &MM_KIND O
> RADIUS .73
> &END MM_KIND
> &END QMMM
>
> &DFT
> CHARGE 4
> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
> POTENTIAL_FILE_NAME ./GTH_POTENTIALS
> # WFN_RESTART_FILE_NAME ./${NAME}_${PREV}.RESTART
> &MGRID
> CUTOFF 300
> COMMENSURATE
> &RS_GRID
> DISTRIBUTION_TYPE DISTRIBUTED
> &END RS_GRID
> &END MGRID
> &QS
> METHOD GPW
> EPS_DEFAULT 1.0E-12
> WF_INTERPOLATION ASPC
> EXTRAPOLATION_ORDER 4
> &END QS
> &SCF
> SCF_GUESS RESTART
> MAX_SCF 40
> EPS_SCF 5.0e-7
> &OT ON
> PRECONDITIONER FULL_KINETIC
> MINIMIZER DIIS
> N_DIIS 7
> &END OT
> &OUTER_SCF
> MAX_SCF 10
> EPS_SCF 5.0e-7
> &END OUTER_SCF
> &END SCF
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &vdW_POTENTIAL
> DISPERSION_FUNCTIONAL PAIR_POTENTIAL
> &PAIR_POTENTIAL
> TYPE DFTD3
> PARAMETER_FILE_NAME ./dftd3.dat
> REFERENCE_FUNCTIONAL BLYP
> LONG_RANGE_CORRECTION .TRUE.
> D3_SCALING 1.0 1.094 1.682
> R_CUTOFF 12.
> &END PAIR_POTENTIAL
> &END vdW_POTENTIAL
> &END XC
> &POISSON #???
> PERIODIC Z #???
> POISSON_SOLVER PERIODIC #???
> &END POISSON
> &END DFT
> &MM
> &FORCEFIELD
> PARMTYPE CHM
> PARM_FILE_NAME par_all27_prot_lipid.prm
> &END FORCEFIELD
> &POISSON
> &EWALD
> EWALD_TYPE spme
> ALPHA 0.44
> GMAX 96
> O_SPLINE 6
> &END EWALD
> &END POISSON
> &END MM
> &SUBSYS
> &CELL
> ABC 40.6411 40.6411 33.2518
> PERIODIC XYZ
> &END CELL
> &TOPOLOGY
> COORD_FILE_NAME p.pdb
> COORD_FILE_FORMAT PDB
> CONN_FILE_NAME p.psf
> CONN_FILE_FORMAT UPSF
> &END TOPOLOGY
>
> &KIND H
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND O
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND N
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q5
> &END KIND
> &KIND C
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q4
> &END KIND
> &END SUBSYS
>
> &END FORCE_EVAL
>
>
> &MOTION
> &MD
> TIMESTEP 0.25
> STEPS 10
> ENSEMBLE NVT
> TEMPERATURE 300
> &THERMOSTAT
> TYPE CSVR
> &CSVR
> TIMECON 20
> &END CSVR
> &DEFINE_REGION
> MM_SUBSYS MOLECULAR
> &END DEFINE_REGION
> &DEFINE_REGION
> QM_SUBSYS ATOMIC
> &END DEFINE_REGION
> &END THERMOSTAT
> &END MD
> &PRINT
> &TRAJECTORY SILENT
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =${NAME}_${NEXT}.dcd
> FORMAT DCD
> &END TRAJECTORY
> &RESTART SILENT
> &EACH
> MD ${FREQ}
> &END EACH
> FILENAME =${NAME}_${NEXT}.restart
> &END RESTART
> &END PRINT
> &END MOTION
>
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