Re: spinAngle

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 18 2012 - 13:41:27 CST

OK, I see your problem now. You're using the syntax of distanceZ to define
the axis, via the groups "ref" and "ref2".

spinAngle is defined differently, with an explicit "axis", such as (0, 0,
1) for example, and a single group of atoms, called "atoms", and the
reference coordinates define the rotation. It works the same as
"orientation".

colvar {
    spinAngle {
        axis (xx, yy, zz)
        atoms {
            ....
        }
        refPositionsFile ....
    }
}

On Wed, Jan 18, 2012 at 2:34 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:

> Dear Giacomo,
>
> Sorry for unclear reply. Now I writting clear email. I am trying to
> prepare covarsconfig file in below. But above file is not correct, sorry
> for that. I sent you for understanding my problem.
>
> ---------------------------------------------------------------------------------
> Colvarstrajfrequency 100
> Colvarsrestartfrequency 100
> colvar {
> name us
> spinAngle {
> main {
> atomnumbers { 3639 3648 3649 3646 3644 3645 3642 3640 }
> }
> ref {
> atomnumbers { 3637 3636 3634 3650 3652 }
> }
> ref2 {
> atomnumbers { 3655 3656 3659 3663 3682 }
> }
> }
> }
> harmonic {
> colvars us
> centers 1.31044732921888e+01
> forceConstant 10.0
> }
>
>
> -------------------------------------------------------------------------------------------------
> main and ref atoms indicates the angles of group of atoms and ref2
> indicates axis. Could you please give me suggessions about the correct way
> preparation of covarsconfig file for spinangle, it will be great help for
> me.
>
>
> Have a nice day,
> Thanks again,
> Maiti
>

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