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

[Juerg Hutter]

Hi

0.5 fs is an often used timestep for all atom simulations.
It is adequate for all vibrations including C-H and O-H
stretching. A 1 fs timestep will lead for those high frequency
modes to problems and energy drifts.

regards

Juerg Hutter

----------------------------------------------------------
Juerg Hutter                   Phone : ++41 44 635 4491
Physical Chemistry Institute   FAX   : ++41 44 635 6838
University of Zurich           E-mail: hut... at pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
----------------------------------------------------------


On Wed, 18 Mar 2009, 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
>
> >
>