From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Feb 14 2011 - 10:06:45 CST
The coordinate you describe seems closely related to a torsional angle
("dihedral"). The torsional angle defined by points A-B-C-D is the
angle between vectors BA and CD, projected onto a plane whose normal
is BC. So it is likely that the existing "dihedral" component could be
easily adapted to do what you need. Another consequence is that the
Jacobian contribution is zero.
The more annoying part seems to be the logic, since there are many
ways the axes can be defined. I don't have specific usage cases in
mind, so it's hard to narrow things down.
2011/2/14 Ajasja Ljubetiè <ajasja.ljubetic_at_gmail.com>:
> Dear NAMD developers,
> After a lot of thought I have come to the conclusion that I would really
> need to sample my system along a colvar similar to the phi component of
> polar coordinates.
> The colvar would measure the angle between the projections of a vector and
> a reference vector on a plane.
> A suitable name for the colvar component would be either angleProjection or
> It could except the following parameters:
> main and ref to define the main (measured) vector.
> ref2 or axis to define the reference vector
> ref3 and ref4 or planeAxis to define the normal vector of the plane.
> most probably ref3 and ref would be the same for most cases... Also perhaps
> more discriptive names then ref1, ref2 etc could be used? Perhaps ref1 and
> ref2 for the refrence vector and planeRef1 and planeRef2 for the plane
> The main and the reference vectors are projected to the plane and the angle
> between them is returned as the value of the colvar. The angle would be in
> the range of [0°,360°) or (-180°, +180°] measured in the positive
> orientation from the reference to the main vector.
> Would somebody be willing to help me implement this in NAMD?
> I volunteer to derive the Jacobian in analytical form (needed for ABF), but
> I woudl be really glad if somebody could write the C part.
> Thank you for your help & best regards,
> Ajasja Ljubetiè,
> Young reasercher,
> Laboratory of biophysics,
> Institute Jo¾ef ©tefan,
> Ljubljana, Slovenia
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