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

[Teodoro Laino]

The bug (which was depending on the way of reading natively AMBER prmtop 
files) is now fixed in the CVS (thanks for reporting)!
Just few comments about your QMMM setup.
1) The way it is setup you will hardly have a conserved energy (you have 
a PERIODIC MM) but you don't use the periodic QMMM version (see PERIODIC 
in QMMM). Alternatively you may think about using a spherical cutoff for 
the electrostatic (that is tapering the interaction after a certain cutoff).
2) you may want to specify proper covalent radius for the QMMM 
electrostatic interactions (at the moment you rely on the default which 
is 0.78 (if I'm not wrong) for all atoms).

Have a nice QMMM.
Teo

p.s.: about the xc_deriv and xc_smooth_rho I would not suggest you to 
use them unless you really know what you are doing. Most of the time you 
don't need to specify those keywords (only for few pathological cases. 
CH4 or H2O are definitely not one of them).


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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