[CP2K:1899] methane in a water box QM/MM

[Teodoro Laino]

Hi Marius,

you catched another bug connected with the new AMBER parsing feature 
when using QMMM.
I'm working right now on a patch.
I will be back to you soon!
Thanks
Teo

Marius Retegan wrote:
> Hi,
>
> In my continuing saga of using cp2k for running qm/mm calculations I 
> have encounter yet another bump.
> While using the input below I get this error "FORCEFIELD| Missing Bond 
>              (  CT,  HC)" and angle ...
>
> &GLOBAL
>   PROJECT mebox_qmmm
>   RUN_TYPE MD
>   PRINT_LEVEL LOW
> &END GLOBAL
>
> &MOTION
>   &MD
>    ENSEMBLE NVT
>    STEPS 1000
>    TIMESTEP 1.0
>    TEMPERATURE 298
>    &THERMOSTAT
>      REGION GLOBAL
>      TYPE CSVR
>      &CSVR
>        TIMECON 100
>      &END CSVR
>    &END THERMOSTAT
>   &END MD
>   &PRINT
>     &RESTART OFF
>     &END RESTART
>     &RESTART_HISTORY OFF
>     &END RESTART_HISTORY
>   &END PRINT
> &END MOTION
>
> &FORCE_EVAL
>   METHOD QMMM
>  
>   &DFT
>     CHARGE 0
>     BASIS_SET_FILE_NAME         GTH_BASIS_SETS
>     POTENTIAL_FILE_NAME         GTH_POTENTIALS
>     &MGRID
>       CUTOFF 280
>       COMMENSURATE
>     &END MGRID
>     &SCF
>       MAX_SCF     20
>       EPS_SCF     1.0E-6
>       &OT T
>         PRECONDITIONER FULL_ALL
>         MINIMIZER DIIS
>       &END OT
>       &PRINT
>         &RESTART OFF
>         &END RESTART
>         &RESTART_HISTORY OFF
>         &END RESTART_HISTORY
>       &END PRINT
>     &END SCF
>     &QS
>       EPS_DEFAULT 1.0E-12
>       MAP_CONSISTENT
>       EXTRAPOLATION ASPC
>       EXTRAPOLATION_ORDER 3
>     &END QS
>     &XC
>       &XC_GRID
>         XC_SMOOTH_RHO NN10
>         XC_DERIV NN10_SMOOTH
>       &END XC_GRID
>       &XC_FUNCTIONAL BLYP
>       &END XC_FUNCTIONAL
>     &END XC
>     &POISSON
>       POISSON_SOLVER MULTIPOLE
>       PERIODIC NONE
>     &END POISSON
>   &END DFT
>  
>   &MM
>     &FORCEFIELD
>       VDW_SCALE14 0.5
>       EI_SCALE14  0.8333333
>       SCALE_CUTOFF .FALSE.
>       PARM_FILE_NAME mebox.prmtop
>       PARMTYPE AMBER   
>       &SPLINE
>         EMAX_SPLINE 1.0
>         RCUT_NB 10
>       &END
>     &END FORCEFIELD
>     &POISSON
>       &EWALD
>         EWALD_TYPE SPME
>         ALPHA .36
>         GMAX 23 23 23
>       &END EWALD
>     &END POISSON
>   &END MM
>  
>   &QMMM
>     E_COUPL GAUSS
>     USE_GEEP_LIB  7
>     &CELL
>       ABC 8.0 8.0 8.0
>       PERIODIC NONE
>     &END CELL
>     &QM_KIND C
>       MM_INDEX 1
>     &END QM_KIND
>     &QM_KIND H
>       MM_INDEX 2 3 4 5
>     &END QM_KIND
>   &END QMMM
>
>   &SUBSYS
>     &CELL
>       ABC [angstrom] 23.2782522  22.7141099  23.2326917 
>       PERIODIC XYZ
>     &END CELL
>     &TOPOLOGY
>       COORDINATE PDB
>       COORD_FILE_NAME mebox_npt.pdb
>       CONNECTIVITY AMBER
>       CONN_FILE_NAME mebox.prmtop
>     &END
>     &KIND C
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q4
>     &END KIND
>     &KIND H
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-BLYP-q1
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> If I change QMMM with FIST the input runs.
>
> I also have some additional questions, but on somewhat different matters.
>
> In the latest papers that I could find that use cp2k to do qm/mm 
> calculations (http://dx.doi.org/10.1021/ja076081h and 
> http://dx.doi.org/10.1021/jp074858n) the authors used a integration 
> step of 0.5 and 0.48. Unfortunately, they did not discussed their 
> choice. I'm used to running qm/mm md with other packages, but I've 
> always used an integration step of 1 fs. Is cp2k different :-)?
>
> Is there any place where I can find information regarding the 
> parameters xc_deriv and xc_smooth_rho and are "good" choices?
>
> Thanks,
> Marius
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