From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon May 11 2015 - 08:57:41 CDT
Thanks a lot, I will try the cv command.
>
> The molecule I wish to compute the spin angle from is a membrane protein
> (so the z axis could probably work), however I am curious: which axis does
> the colvar module use by default ?
>
"tilt" shares options with "spinAngle": the default axis for both is stated
in the documentation.
2015-05-11 15:40 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>
>> Hello Marlon, without any other information about the system, the choice
>> of axis is up to you: ideally, the axis would represent a preferential
>> direction in your system, e.g. because a certain molecule is elongated in
>> shape.
>>
>> To recalculate the value of collective variables of interest, you can now
>> use the "cv" command inside VMD. Version 1.9.2 has a preliminary version
>> of this command, the alpha version of 1.9.3 has a much better working
>> version.
>>
>> On Mon, May 11, 2015 at 4:51 AM, Marlon SIDORE <marlon.sidore_at_gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I have been trying to recalculate (using my own scripts) the value of
>>> the spin angle along a trajectory for trajectories where the collective
>>> variable was not set. As the collective variable is only a subset of the
>>> orientation colvar, I tried to calculate it.
>>>
>>> I could use the 2004 paper (Using quaternions to calculate RMSD) to
>>> obtain the particular quaternion (which corresponds to the sought rotation)
>>> ... However I have been stuck for a while at this step, probably due to a
>>> lack of maths training.
>>>
>>> The colvars manual says that this rotation corresponds to two rotations,
>>> a rotation around an axis and a tilt rotation around an axis orthogonal to
>>> the previous axis. The rotation I need (the spin angle) is the first one.
>>>
>>> It seems that I need to know the axis beforehand: how ? And once I have
>>> it, there's a formula to get the rotation given this axis, but do I need to
>>> do something more to differentiate the rotation from the tilt ?
>>>
>>> Thanks for your attention, and sorry if it all comes down to my lack of
>>> math training.
>>> Best regards,
>>>
>>> Marlon Sidore
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Assistant Professor of Research
>> Institute for Computational Molecular Science (ICMS)
>> College of Science and Technology, Temple University
>> 1925 North 12th Street (035-07), Room 704D
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213
>> https://icms.cst.temple.edu/members.html
>> http://giacomofiorin.github.io/
>>
>>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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