From: Marlon SIDORE (marlon.sidore_at_gmail.com)
Date: Mon May 11 2015 - 08:48:51 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 ?
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
> 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
> On Mon, May 11, 2015 at 4:51 AM, Marlon SIDORE <marlon.sidore_at_gmail.com>
>> 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
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