[CP2K:8392] Re: CONDITIONED_DISTANCE COLVAR

Nitish Govindarajan gnitis... at gmail.com
Wed Nov 16 19:05:53 CET 2016


P.S. I'd like to use this as a way to recognise a OH- ion in solution. It
seems to work when I have to identify the highest coordinated atom to say
235 in the example. But I'd like to identify lowest coordinated atom (the
OH- ion) and then use this to compute the distance between this atom and
atom 235. I'm not sure if this CV can be used to do that


On Sun, Nov 13, 2016 at 1:24 AM, Nitish Govindarajan <gnitis... at gmail.com
> wrote:

> Thanks a lot for your reply marcella. I changed the parameters but I still
> find that after the first SCF cycle, the output just hangs. So I'm not sure
> what is wrong.
>
> Thanks
> Nitish
>
> On Sat, Nov 12, 2016 at 12:27 PM, Marcella Iannuzzi <marci... at gmail.com
> > wrote:
>
>> Hi Nitish,
>>
>> yes this variable has been successfully used.
>> It is meant to calculate the distance between one atom and one atom taken
>> from another group of atoms.
>> To select the second atom, the coordination function is selected, i.e.,
>> the atom with the largest coordination number is selected.
>> Using an input like
>>
>>     &COLVAR
>>
>>        &CONDITIONED_DISTANCE
>>
>>          ATOMS_DISTANCE  235
>>
>>          KINDS_FROM N
>>
>>          ATOMS_TO  235
>>
>>          R0 [angstrom] 3.00000000E+00
>>
>>          NN  10
>>
>>          ND  16
>>
>>          LAMBDA 100
>>
>>        &END
>>
>>     &END COLVAR
>>
>>
>> The distance is calculated between atom 235 and the N atom that has the
>> largest coordination with atom 235, i.e., the closest to atom 235.
>>
>>
>> Kind regards
>>
>> Marcella
>>
>> On Friday, November 11, 2016 at 1:03:03 PM UTC+1, Nitish Govindarajan
>> wrote:
>>>
>>> Hi everyone,
>>> I was wondering if anyone has tried using the conditioned distance as a
>>> CV in a metadynamics run. I am trying to use this, but I have some
>>> questions on how to define ATOMS_DISTANCE and also the output seems to not
>>> print after the 1st SCF cycle run.
>>>
>>>       &CONDITIONED_DISTANCE
>>>
>>>       ATOMS_DISTANCE 6 2
>>>
>>>       ATOMS_DISTANCE 6 3
>>>
>>>       ATOMS_DISTANCE 6 4
>>>
>>>       ATOMS_DISTANCE 6 5
>>>
>>>       ATOMS_DISTANCE 6 7
>>>
>>>       ATOMS_DISTANCE 6 8
>>>
>>>       ATOMS_DISTANCE 6 9
>>>
>>>       ATOMS_DISTANCE 6 10
>>>
>>>       ATOMS_DISTANCE 6 11
>>>
>>>       ATOMS_DISTANCE 6 12
>>>
>>>       ATOMS_DISTANCE 6 13
>>>
>>>       ATOMS_DISTANCE 6 14
>>>
>>>       ATOMS_DISTANCE 6 15
>>>
>>>       ATOMS_DISTANCE 6 16
>>>
>>>       KINDS_FROM O
>>>
>>>       KINDS_TO H
>>>
>>>       LAMBDA -20
>>>
>>>       ND 32
>>>
>>>       NN 8
>>>
>>>       R0 [angstrom] 1.27
>>>
>>>       &END CONDITIONED_DISTANCE
>>>
>>>
>>> Thanks,
>>>
>>> Nitish
>>>
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>
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