MM_KIND/QM_KIND atom type

Luca bellu... at unisi.it
Fri Sep 21 17:40:05 CEST 2007


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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