[CP2K:2123] Re: assignment of covalent radii for MM atoms

[Marius Retegan]

But why can't the atomic kinds be assigned from the amber parameter file
instead of being automatically generated?

On Wed, Jun 10, 2009 at 4:09 PM, Teodoro Laino <teodor... at gmail.com>wrote:

> 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>http://www.jajah.com/Teo
> E-mail: <teo... at laino.eu>teo... at laino.eu
>              <teodor... at gmail.com>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>
> 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>
>> teodor... at gmail.com
>> > <mailto: <teodor... at gmail.com>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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