MM_KIND/QM_KIND atom type

Luca bellu... at unisi.it
Fri Sep 21 18:00:59 CEST 2007


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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