# Re: angle between 2 vectors as collective variable

Date: Thu Mar 26 2015 - 11:04:09 CDT

Thanks a lot Giacomo,

Yes, indeed I was referring to the less simple case ... I will try your suggestion as soon as I'll be back to the lab on the 7th of april.

Thanks again

On March 26, 2015 4:16:25 PM CET, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>So, obviously "angle" function is what you're looking for if you have
>three
>groups (A, B, and C) and you want to calculate the angle between the
>B-->A
>vector and the B-->C vector.
>
>than
>that, where the "B" group isn't shared, but you have four independent
>groups, and the vectors are B-->A and C-->D.
>
>So you can do something like this:
>- translate A so that B is centered on the origin
>- translate D so that C is centered on the origin
>- calculate the angle between the origin-->A vector and the origin-->D
>vector
>
>You can do that with centerReference, which allows you to translate the
>positions of a group (e.g. the A group), and refPositionsGroup, which
>allows you to use an additional group for the fitting (e.g. the B
>group).
>
>colvar {
> angle {
> group1 {
> # define here the "A" group
> centerReference yes
> rotateReference no
> refPositionsGroup {
> # define here the "B" group
> }
> refPositionsFile file.pdb # a set of positions for "B" that is
>centered on the origin
> }
> group2 { dummyAtom (0, 0, 0) }
> group3 {
> # define here the "D" group
> centerReference yes
> rotateReference no
> refPositionsGroup {
> # define here the "C" group
> }
> refPositionsFile file.pdb # a set of positions for "C" that is
>centered on the origin
> }
> }
>}
>
>Note that you need to disable rotateReference, otherwise the rotational
>fit
>of groups B or C will change the orientation of the vectors.
>
>Giacomo
>
>
>
>
>
>On Thu, Mar 26, 2015 at 11:03 AM, Vlad Cojocaru <
>
>> As distance vectors from positions ...
>>
>>
>> On March 26, 2015 3:58:26 PM CET, Giacomo Fiorin
><giacomo.fiorin_at_gmail.com>
>> wrote:
>>>
>>> Hello Vlad, it depends on how the two vectors are being calculated
>from,
>>> e.g. as distance vectors between two positions or axes of rotation.
>>>
>>> Giacomo
>>>
>>> On Thu, Mar 26, 2015 at 10:17 AM, Vlad Cojocaru <
>>>
>>>> Dear all,
>>>>
>>>> This might be a trivial question but somehow I am not able to find
>an
>>>> answer to it. Is it possible to define the angle between 2 vectors
>as
>>>> collective variable within the COLVAR module ?
>>>>
>>>> Thanks for any tips
>>>>
>>>> Best wishes
>>>>
>>>> --
>>>> Computational Structural Biology Laboratory
>>>> Department of Cell and Developmental Biology
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>
>>>>
>>>
>>>
>> --
>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>
>
>
>
>--
>Giacomo Fiorin
>Assistant Professor of Research
>Institute for Computational Molecular Science (ICMS)
>College of Science and Technology, Temple University
>1925 North 12th Street (035-07), Room 704D
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