Re: calculation of helical axis in NAMD

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Apr 09 2018 - 10:29:11 CDT

Thanks Jerome, Joshua
                                       its very helpful.

thank you
Dhiraj

On Mon, Apr 9, 2018 at 10:21 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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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