From: Marlon SIDORE (marlon.sidore_at_gmail.com)
Date: Mon May 11 2015 - 09:06:46 CDT
Thanks a lot, I should have thought about that.
2015-05-11 15:57 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> 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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