MM_KIND/QM_KIND atom type

Luca bellu... at unisi.it
Tue Oct 2 14:06:20 CEST 2007


I Fawzi,
it was only a fast test for QMMM procedure and with COMMENSURATE
keyword "works".
I have in mind a cutoff of 260-280 Ry
or greater, for organic molecules with H,C,O,N atom kind. Is it right?
....but I am going to
read article "QUICKSTEP: Fast and accurate....."
for more details.

Thanks,
Luca

On Oct 2, 11:34 am, Fawzi Mohamed <fa... at gmx.ch> wrote:
> The grids have to be commensurate for QMMM (keword COMMENSURATE).
> by the way you know that a cutoff of 140 Ry is waaay to small for
> GPW, and you might want to write
> MM_INDEX 6 7 8, I am not sure that repeating the keyword does what
> you want.
>
> Fawzi
> On Sep 21, 2007, at 6:00 PM, Luca wrote:
>
>
>
> > E
> > A this point I have :
> > QS ok it work
> > Fist OK it Work
> > QMMM do NOT Work
>
> > Problem is:
> >  ERROR in pw_spline_utils:add_coarse2fine processor
> > Thanks in advance for any help.
>
> > My INPUT:
>
> > &FORCE_EVAL
> >  METHOD QMMM
> >  &DFT
> >     BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
> >     POTENTIAL_FILE_NAME ./GTH_POTENTIALS
> >     &MGRID
> >       CUTOFF 140
> >     &END MGRID
> >     &SCF
> >       SCF_GUESS ATOMIC
> >     &END SCF
> >     &XC
> >       &XC_FUNCTIONAL BLYP
> >       &END XC_FUNCTIONAL
> >     &END XC
> >   &END DFT
>
> >   &MM
> >     &FORCEFIELD
> >        PARM_FILE_NAME  par-amber.imp
> >        PARMTYPE CHM
> >     &END FORCEFIELD
> >     &POISSON
> >       &EWALD
> >         EWALD_TYPE SPME
> >         ALPHA .44
> >         GMAX 32
> >         O_SPLINE 6
> >       &END EWALD
> >     &END POISSON
> >   &END MM
>
> >  &QMMM
> >     MM_POTENTIAL_FILE_NAME MM_POTENTIAL
> >     &CELL
> >      UNITS ANGSTROM
> >      ABC 6.0 6.0 6.0
> >     &END CELL
> >     ECOUPL GAUSS
> >     NOCENTER
> >     USE_GEEP_LIB 8
>
> >     &MM_KIND HW
> >       RADIUS 0.44
> >     &END MM_KIND
>
> >     &MM_KIND OW
> >       RADIUS 0.780
> >     &END MM_KIND
>
> >     &QM_KIND C
> >         MM_INDEX 5
> >     &END QM_KIND
>
> >     &QM_KIND C
> >         MM_INDEX 4
> >     &END QM_KIND
>
> >     &QM_KIND C
> >         MM_INDEX 3
> >     &END QM_KIND
>
> >     &QM_KIND H
> >         MM_INDEX 6
> >         MM_INDEX 7
> >         MM_INDEX 8
> >     &END QM_KIND
>
> >     &QM_KIND O
> >         MM_INDEX 1
> >     &END QM_KIND
>
> >     &QM_KIND N
> >         MM_INDEX 2
> >     &END QM_KIND
>
> >   &END
>
> >   &SUBSYS
> >     &CELL
> >       ABC 13.0 13.0 13.0
> >       UNIT ANGSTROM
> >     &END CELL
>
> >     &TOPOLOGY
> >       COORD_FILE_NAME isox_pos_a.pdb
> >       COORDINATE PDB
> >       CONN_FILE_NAME isox_pos_a.psf
> >       CONNECTIVITY PSF
> >     &END TOPOLOGY
>
> >     &KIND H
> >       BASIS_SET    DZVP-GTH
> >       POTENTIAL    GTH-BLYP-q1
> >     &END KIND
>
> >     &KIND O
> >       BASIS_SET    DZVP-GTH
> >       POTENTIAL    GTH-BLYP-q6
> >     &END KIND
>
> >     &KIND C
> >       BASIS_SET    DZVP-GTH
> >       POTENTIAL    GTH-BLYP-q4
> >     &END KIND
>
> >     &KIND N
> >       BASIS_SET    DZVP-GTH
> >       POTENTIAL    GTH-BLYP-q5
> >     &END KIND
>
> >   &END SUBSYS
> > &END FORCE_EVAL
>
> > &GLOBAL
> >   FFTLIB FFTSG
> >   PROJECT ISOXA2
> >   RUN_TYPE MD
> >   PRINT_LEVEL LOW
> > &END GLOBAL
>
> > &MOTION
> >   &MD
> >     ENSEMBLE NVE
> >     STEPS 100
> >     TIMESTEP 0.5
> >     TEMPERATURE 300.0
> >   &END MD
> > &END MOTION
>
> > On 21 Set, 17:40, Luca <bellu... at unisi.it> wrote:
> >> OK.
> >> Thank you
> >> Luca
>
> >> On 21 Set, 17:26, Teodoro Laino <teodor... at gmail.com> wrote:
>
> >>> Yes.. it's the 6th column of PSF.. the 5th is the atom_name..
>
> >>> On 21 Sep 2007, at 17:20, Luca wrote:
>
> >>>> I don't understand...for atom_type I mean AMBER(FF)_atom_type
> >>>> For example. My PSF file:
> >>>>        1 O1   1    IXA  O    OS    -0.121300
> >>>> 16.0000           0
> >>>>        2 O1   1    IXA  N    NB    -0.400600
> >>>> 14.0100           0
> >>>>     ..............
> >>>>        9 W1   2  TIP3 OH2  OW    -0.834000
> >>>> 16.0000           0
> >>>>       10 W1  2  TIP3 H1   HW     0.417000        1.0080           0
> >>>>       11 W1  2  TIP3 H2   HW     0.417000        1.0080           0
>
> >>> this is ok.. because you're referring to the KIND read from the
> >>> connectivity file..
>
> >>>>   For MM water I should write:
> >>>>   MM_KIND OW
> >>>>     RADIUS.....
> >>>>   END
> >>>>   MM_KIND HW
>
> >>> For QM_KIND you can use whatever LABEL you like.. the important
> >>> thing
> >>> is that this one has to match the one
> >>> of the KIND section of the SUBSYS section.. as all QS input files..
>
> >>>>    .....
> >>>>   END
> >>>>   QM_KIND OS
> >>>>       MM_INDEX 1
> >>>>   END
>
> >>> Teo
>
> >>>> etc.....
>
> >>>> On 21 Set, 16:57, Teodoro Laino <teodor... at gmail.com> wrote:
> >>>>> The rule is that in cp2k we loose any information about
> >>>>> atom_name..
> >>>>> we only work with the atom_type.
> >>>>> This is valid then for MM_KIND, QM_KIND and KIND in subsys.
>
> >>>>> Teo
>
> >>>>> On 21 Sep 2007, at 16:30, Luca Bellucci wrote:
>
> >>>>>> Hi all,
> >>>>>> when I use PSF and PDB file for connectivity and coordinates I
> >>>>>> can
> >>>>>> use atom_type or atom_name  for define MM_KIND and QM_KIND.
> >>>>>> The same thing happens in section SUBSYS with KIND key.
> >>>>>> Is there a rule?
> >>>>>> Thanks




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