[CP2K:2119] Re: assignment of covalent radii for MM atoms

Marius Retegan marius.s... at gmail.com
Tue Jun 9 18:03:24 CEST 2009


On Tue, Jun 9, 2009 at 5:35 PM, Teodoro Laino <teodor... at gmail.com>wrote:

>
> By default all atoms have the same covalent radius.


I got this.


> Please use the tools provided by Axel and the CMM folks
> (covalent_radii.pl, you can get here in this group under Files) if you
> want realistic values.


What confused me is that the input that I was referring to has the following
section:
    &MM_KIND H
      RADIUS 0.440
    &END MM_KIND
    &MM_KIND O
      RADIUS 0.780
    &END MM_KIND
With this all atoms get the same radii. So this part of the input it's
useless.
If I change it to HT and OT I get the expected values.
Marius


>
> Regards
> Teo
>
> Marius Retegan wrote:
> > Apparently cp2k assigns the same covalent radius for the MM atoms.
> > I took the input file from tests/QMMM/QS/regtest-4/wat_nacl.inp and
> > changed the print level to medium.
> > This is what I get:
> >
> >      MM    POINT CHARGES GENERATING THE QM/MM ELECTROSTATIC POTENTIAL
> >
> >
>  -------------------------------------------------------------------------
> >         MM ATOM:    3 RADIUS:    1.511781 CHARGE:    0.417000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    4 RADIUS:    1.511781 CHARGE:   -0.834000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    5 RADIUS:    1.511781 CHARGE:    0.417000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    6 RADIUS:    1.511781 CHARGE:    0.417000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    7 RADIUS:    1.511781 CHARGE:   -0.834000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    8 RADIUS:    1.511781 CHARGE:    0.417000CORR.
> > RADIUS    1.511781
> >         MM ATOM:    9 RADIUS:    1.511781 CHARGE:    0.417000CORR.
> > RADIUS    1.511781
> >         MM ATOM:   10 RADIUS:    1.511781 CHARGE:    1.000000CORR.
> > RADIUS    1.511781
> >         MM ATOM:   11 RADIUS:    1.511781 CHARGE:   -1.000000CORR.
> > RADIUS    1.511781
> >
> > Atom 3 is an oxygen, while 4 if a hydrogen. Is this related to
> > periodic QM/MM?
> > Thanks
> > Marius
> >
> > >
>
>
> >
>
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