[CP2K:2120] Re: assignment of covalent radii for MM atoms

Teodoro Laino teodor... at gmail.com
Tue Jun 9 18:12:38 CEST 2009


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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