[CP2K:2680] Re: Bond rotation restraint

Teodoro Laino teodor... at gmail.com
Wed Apr 21 17:29:01 CEST 2010


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
>>>>>           
>>>>> --
>>>>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>> To unsubscribe from this group, send email to cp2k+uns... at googlegroups.com.
>>>>> For more options, visit this group athttp://groups.google.com/group/cp2k?hl=en.
>>>>>           
>>>> --
>>>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>>>> To post to this group, send email to cp... at googlegroups.com.
>>>> To unsubscribe from this group, send email to cp2k+uns... at googlegroups.com.
>>>> For more options, visit this group athttp://groups.google.com/group/cp2k?hl=en.
>>>>         
>>> --
>>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>>> To post to this group, send email to cp... at googlegroups.com.
>>> To unsubscribe from this group, send email to cp2k+uns... at googlegroups.com.
>>> For more options, visit this group athttp://groups.google.com/group/cp2k?hl=en.
>>>       
>> --
>> You received this message because you are subscribed to the Google Groups "cp2k" group.
>> To post to this group, send email to cp... at googlegroups.com.
>> To unsubscribe from this group, send email to cp2k+uns... at googlegroups.com.
>> For more options, visit this group athttp://groups.google.com/group/cp2k?hl=en.
>>     
>
>   

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To post to this group, send email to cp... at googlegroups.com.
To unsubscribe from this group, send email to cp2k+uns... at googlegroups.com.
For more options, visit this group at http://groups.google.com/group/cp2k?hl=en.




More information about the CP2K-user mailing list