RE: spinAngle

From: Buddhadev Maiti (bmaiti_at_gsu.edu)
Date: Wed Jan 18 2012 - 16:28:58 CST

Dear Giacomo,

Thank you very much for your great help. Now it is clear for me. I have another question if I am not bothering you, if there is NAMD implementation of covar varible for simple rotation around the pivot point without fitting. Could you please give me reply, ti will be great help for me.

Have a nice day,
Thanks again,
Maiti
________________________________
From: Giacomo Fiorin [giacomo.fiorin_at_gmail.com]
Sent: Wednesday, January 18, 2012 2:41 PM
To: Buddhadev Maiti
Cc: namd-l
Subject: Re: spinAngle

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<mailto: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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