Re: whidth value of orientation in colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 10 2014 - 16:20:45 CST

Orientation has quaternion values on the 4-dimensional unit sphere, and the
distance between two different orientations is the angle between the two
quaternions on that sphere (in radians). Because of symmetry a quaternion
and its opposite are the same rotation so a 30° rotation will be 15° away
from the quaternion that represents the identity (convert in radians of
course).

See the following paper and the Coutsias reference therein:
http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.813594

Bests
Giacomo
 On Jan 9, 2014 7:28 PM, "서용일" <seoyi86_at_gmail.com> wrote:

> Fiorin, I'm sorry that my mistake. I want to know unit of width, not
> "tilt" but "orientation".
>
> colvar {
> name Rotation_ring
>
> width 1.0 <-- what is unit of width?
>
> orientation {
> atoms {
> psfSegID 8RA
> atomNameResidueRange CA 1 - 8
> }
> refPositionsFile ../lt8mer.all.colvars.namd.coor
> refPositionsCol B
> }
> }
>
> Yongil
>
>
> 2014/1/9 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>
>> Yongil, the "tilt" variable is the cosine of the tilt angle. So the
>> whole interval of values is -1 to 1. Cos(0) = 1.00 and cos(30) = 0.86, so
>> you want the width to be small enough to distinguish well between those two
>> values (e.g. width = 0.01).
>>
>> Giacomo
>>
>>
>> On Thu, Jan 9, 2014 at 3:27 AM, 서용일 <seoyi86_at_gmail.com> wrote:
>>
>>> Dear NAMD users
>>>
>>> Hi, I'm using orientation component in colvars module for control of
>>> protein's tilt angle.
>>> I try to rotation of protein's tilt angle from 0 degree to 30 degree.
>>> But, I don't know value of width in orientation either degree or radian--089e012940d830dadb04efa523a7--

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