[gmx-users] bending angle between 2 vectors defined by cm of groups of atoms

[Teemu Murtola]

Hi,

On Wed, May 15, 2013 at 7:13 PM, battistia at libero.it <battistia at libero.it>wrote:

> do you know if it is possible make the bending angle calculation in the
> following case?
>
> I have got three groups (G1, G2, G3) into a system.
>  I have to define the center of mass of each one. I have to calculate the
> bending angle defined by vector 1 and vector 2.
> vector 1:  by the center of mass of G1 to the center of mass of G2.vector
> 2:  by the center of mass of G2 to the center of mass of G3
>
> Is it possible do this calculation with gromacs?
>

I don't think this is easily possible with any tool in Gromacs 4.5 or 4.6.
It should be possible with a work-in-progress tool in the development
branch, though. If you want to give it a try, you can compile the master
branch from git and check out 'gmx gangle -h'. No warranties that it works;
please report any issues.

Best regards,
Teemu