RE: calculation of helical axis in NAMD

From: Vermaas, Joshua (
Date: Sat Apr 07 2018 - 10:01:45 CDT

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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