**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Thu Mar 26 2015 - 10:16:25 CDT

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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.

Because you're asking about this you probably have a less simple case 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 <

vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:

*> As distance vectors from positions ...
*

*>
*

*> Vlad
*

*>
*

*> 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 <
*

*>> vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
*

*>>
*

*>>> 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
*

*>>> Vlad
*

*>>>
*

*>>> --
*

*>>> Dr. Vlad Cojocaru
*

*>>> 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
*

*>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
*

*>>> 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 Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/

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