Re: calculation of helical axis in NAMD

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Apr 09 2018 - 10:21:26 CDT

You can ensure that one helix rotates strictly with respect to the rest of
the protein by calculating the spinAngle coordinate in the frame of
reference of the rest of the protein. See centerReference, rotateReference.
This will account for the rotation of the axis with the overall rotation of
the protein. It will not account for the moving helix tilting with respect
to the protein though. That seems more complicated to account for.

Best,
Jerome

On 9 April 2018 at 01:28, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:

> 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!
>
> -Josh
>
>
>
> 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
> 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.
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.12%2Fug%2Fnode57.html%23SECTION0001341240000000000000.&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C8d7be7f2db1c4a175e1008d59da1eabb%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636588241113888037&sdata=AXR4ZAbgyLdQRm3n1NDOp8rljFf%2FiTFf8O%2FNi4h3yTQ%3D&reserved=0>
>> 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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