[CP2K:2121] Re: assignment of covalent radii for MM atoms

[Marius Retegan]

Hi,

When using amber parameter files the atomic kind name
is automatically generated and is different from the atomic
kinds in the amber force field. Is it possible to change this behaviour?

Thanks
Marius

On Tue, Jun 9, 2009 at 6:12 PM, Teodoro Laino <teodor... at gmail.com>wrote:

>
> Regtests are there not to provide meaningful example but for checking
> integrity while developing.
> In this case that regtest is testing something totally different than
> the covalent radius for QMMM.
> As you realized by yourself, if you provide the correct types, the right
> radius will be parsed and used.
>
> Teo
>
>
> Marius Retegan wrote:
> >
> >
> > On Tue, Jun 9, 2009 at 5:35 PM, Teodoro Laino <teodor... at gmail.com
> > <mailto: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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