RE: calculation of helical axis in NAMD

From: Vermaas, Joshua (
Date: Sun Apr 08 2018 - 18:28:10 CDT

To get the rotation axis, I took the largest moment of inertia vector for the alpha helix, and used that to define my axis. I didn't bother updating the axis, since it didn't vary that much over the 100ps of simulation I used to drive the transition I was looking for. The spinAngle collective variable kind of assumes your axis doesn't change (although Giacomo or Jerome might have other ideas). If you want to track the exact orientation, the "orientation" collective variable might suit your needs better, since it doesn't need to define an axis at all!


On 2018-04-08 16:41:52-06:00 Dhiraj Srivastava wrote:

thanks Joshua
                       How did you calculated the rotation axis? is there a way I can calculate it while doing the simulation so that it can keeps getting updated? I do want to keep the flexibility of alpha helix during simulation so the helix's principle axis will be changing during course of simulation.
thank you

On Sat, Apr 7, 2018 at 10:01 AM, Vermaas, Joshua <<>> wrote:
See> This is an example from a system I was working on, where I wanted to change the rotation of a helix by 30 degrees. The helix was tagged with a 1 in the beta column of spin.pdb.

colvar {
        name spin
        spinAngle {
                atoms {
                        atomsFile spin.pdb
                        atomsCol B
                        atomsColValue 1
                refPositionsFile spin.pdb
                refPositionsCol B
                refPositionsColValue 1
                axis (-0.05879103049526372, 0.37592884870839527, 0.9247816582534958)
harmonic {
        name harm
        colvars spin
        forceConstant 1000
        centers 0
        targetCenters -30
        targetNumSteps 50000


On 2018-04-07 00:06:39-06:00<> wrote:

   I want to calculate helical axis of an alpha-helix of my protein along which I want to rotate that particular helix with respect to rest of the protein. is there any build in function in namd that I can use to calculate it or do I need to write the script to do it? also during the simulation, the atoms in alpha helix will move, changing the helical axis. so do I need to keeps calculating and updating the axis of rotation or will it be safe to calculate it at the beginning of the simulation and don't change it during the simulation? if I am calculating the helical axis on the the fly during simulation, will it slow down the simulation significantly?
Thank you

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