[CP2K:2124] Re: assignment of covalent radii for MM atoms

Teodoro Laino teodor... at gmail.com
Wed Jun 10 16:24:38 CEST 2009


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
E-mail: teo... at laino.eu
              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 
> > 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
> 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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