[CP2K:2122] Re: assignment of covalent radii for MM atoms

[Teodoro Laino]

No, for varius reasons of compatibility between AMBER and CHARMM  
(which is the FF natively supported) this is not possible.

---------------------------------------------
Teodoro Laino
Zurich Switzerland

Contact info:
Tel.:     http://www.jajah.com/Teo
E-mail: teo... at laino.eu
              teodor... at gmail.com
---------------------------------------------

On 10 Jun 2009, at 16:06, Marius Retegan <marius.s... at gmail.com>  
wrote:

> 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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