[CP2K:2125] Re: assignment of covalent radii for MM atoms

Marius Retegan marius.s... at gmail.com
Wed Jun 10 17:25:06 CEST 2009


So if I want to use amber topologies can you think of an "easy" method for
preparing the input files for QM/MM calculations?
Also even if I don't assign any kinds to mm atoms I get this error message:

*
 *** ERROR in read_atomic_kind (MODULE atomic_kind_types)  ***
 *


 *** No &KIND section was possible to associate to the atomic kind <O>.
***
 *** The KIND section were also scanned for the corresponding element <O>
***
 *** and for the DEFAULT section but no match was found. Check your input
***
 *** file!
***


 *** Program stopped at line number 1538 of MODULE atomic_kind_types  ***

 ===== Routine Calling Stack =====

            5 read_atomic_kind
            4 read_atomic_kind_set
            3 quickstep_create_force_env
            2 qmmm_create_force_env
            1 CP2K
 CP2K| Abnormal program termination, stopped by process number 0

Thanks
Marius

On Wed, Jun 10, 2009 at 4:24 PM, Teodoro Laino <teodor... at gmail.com>wrote:

> Because for CP2K a kind has a specific charge. Same kinds have same charge.
> For amber the charge has nothing to do with the kinds, i.e. same kinds can
> have different charges.
>
> ---------------------------------------------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 16:12, Marius Retegan <marius.s... at gmail.com>
> wrote:
>
> 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>
> 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>
>> http://www.jajah.com/Teo
>> E-mail: <teo... at laino.eu> <teo... at laino.eu>teo... at laino.eu
>>              <teodor... at gmail.com> <teodor... at gmail.com>
>> teodor... at gmail.com
>> ---------------------------------------------
>>
>> On 10 Jun 2009, at 16:06, Marius Retegan < <marius.s... at gmail.com>
>> 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>
>> 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>
>>> teodor... at gmail.com
>>> > <mailto: <teodor... at gmail.com> <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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