Re: calculation of helical axis in NAMD

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sun Apr 08 2018 - 17:41:48 CDT

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
Dhiraj

On Sat, Apr 7, 2018 at 10:01 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> See http://www.ks.uiuc.edu/Research/namd/2.12/ug/node57.html#
> SECTION0001341240000000000000. 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
> }
>
> -Josh
>
>
>
>
> On 2018-04-07 00:06:39-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi
> 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
> Dhiraj
>
>

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