[CP2K:2680] Re: Bond rotation restraint

[Teodoro Laino]

Looks (apparently) correct.
Teo

Ilya wrote:
>> can you please post the URL of the input reference page where you found
>>     
>
> http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/BOND_ROTATION.html
>
> How to set a restraint for the rotation of a bond, e.g. atom12-atom13,
> in respect to the line, which is parallel to some axis, e.g. [0,0,1]?
>
> Does it look like this:
>    ...
>    &SUBSYS
>    ...
>      &COLVAR
>          &BOND_ROTATION
>            &POINT
>               ATOMS 12
>               TYPE GEO_CENTER
>            &END POINT
>            &POINT
>               ATOMS 13
>               TYPE GEO_CENTER
>            &END POINT
>            &POINT
>               XYZ 0.0 0.0 0.0
>               TYPE FIX_POINT
>            &END POINT
>            &POINT
>               XYZ 0.0 0.0 1.0
>               TYPE FIX_POINT
>            &END POINT
>            P1_BOND1 1
>            P2_BOND1 2
>            P1_BOND2 3
>            P2_BOND2 4
>          &END BOND_ROTATION
>      &END COLVAR
>    &END SUBSYS
>
> ?
>
> Sincerely,
> Ilya
>
>
> On 21 апр, 18:00, Ilya <ikupc... at gmail.com> wrote:
>   
>> Sorry, I have not noticed your messages, since I was "encrypting" my
>> own one.
>>
>> Thanks a lot for an instant reply.
>> I beg your pardon for my English.
>> I am working on it.
>>
>> Sincerely,
>> Ilya
>>
>> On 21 апр, 17:53, Ilya <ikupc... at gmail.com> wrote:
>>
>>
>>
>>     
>>> Please, help me.
>>>       
>>> I send a sample file if needed.
>>>       
>>> And, could someone explain what are the values used in "(X-X0)" in
>>> case of an angle(rotational?) restraint? Angle values or cos/sin?
>>> An if values are implied what are the units - degrees, radians, pi?
>>>       
>>> Sincerely,
>>> Ilya
>>>       
>>> On 21 апр, 16:04, Ilya <ikupc... at gmail.com> wrote:
>>>       
>>>> If use 2 bonds restraint, the bonds are in different parts of system
>>>> and not connected i.e. I can not apply common angle or torsional
>>>> restraints.
>>>>         
>>>> On 21 апр, 16:00, Ilya <ikupc... at gmail.com> wrote:
>>>>         
>>>>> Hello.
>>>>>           
>>>>> I would like to set a restraint for the angle between two bonds, or
>>>>> better between a bond and Z axis.
>>>>>           
>>>>> I use the following keys:
>>>>>           
>>>>>    &SUBSYS
>>>>>     ...
>>>>>    &COLVAR
>>>>>        &BOND_ROTATION
>>>>>             P1_BOND1 86 #these are atom indexes
>>>>>             P1_BOND2 12
>>>>>             P2_BOND1 85
>>>>>             P2_BOND2 13
>>>>>       &END BOND_ROTATION
>>>>>      &END COLVAR
>>>>>    &END SUBSYS
>>>>>    ...
>>>>>    &CONSTRAINT
>>>>>      &COLLECTIVE
>>>>>        TARGET   0.0
>>>>>        MOLNAME q1010c-dyn
>>>>>        COLVAR 1
>>>>>        &RESTRAINT
>>>>>           k [kjmol] 1.0
>>>>>        &END RESTRAINT
>>>>>      &END COLLECTIVE
>>>>>    &END CONSTRAINT
>>>>>           
>>>>> But I can not see any effect during my MD.
>>>>> I have single molecule in system called "q1010c-dyn"
>>>>>           
>>>>> Could anyone tell me, should I just increase restraint k value, or
>>>>> change input, or allot 2 molecules instead of 1, or whatever?
>>>>> Just how it should work?
>>>>>           
>>>>> Thanks.
>>>>> Ilya
>>>>>           
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>>     
>
>   

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