MM_KIND/QM_KIND atom type
bellu... at unisi.it
Fri Sep 21 17:40:05 CEST 2007
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
> > 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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