From: Ajasja Ljubetiè (ajasja.ljubetic_at_gmail.com)
Date: Mon Feb 14 2011 - 10:13:28 CST
Thank you both!
This is a great idea and I think I should be able to get the desired result,
since I'm "cheating" a bit and restraining the rotation of the protein so
that I can use fixed reference axes :)
So now I only have to derive the jacobian for the angle colvar and I'm on my
2011/2/14 Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> Hi Ajasja,
> 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
> > a reference vector on a plane.
> > A suitable name for the colvar component would be either angleProjection
> > angleXY.
> > 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
> > more discriptive names then ref1, ref2 etc could be used? Perhaps ref1
> > ref2 for the refrence vector and planeRef1 and planeRef2 for the plane
> > normal?
> > The main and the reference vectors are projected to the plane and the
> > between them is returned as the value of the colvar. The angle would be
> > 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),
> > 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
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:48 CST