[CP2K:1903] Re: methane in a water box QM/MM

[Marius Retegan]

Thanks a lot for all your comments.

Marius

On Wed, Mar 18, 2009 at 5:14 PM, Teodoro Laino <teodor... at gmail.com>wrote:

>
> 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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