New colvar feature request -- angleXY

From: Ajasja Ljubetič (
Date: Mon Feb 14 2011 - 07:19:46 CST

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 normal?

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 Ljubeti,
Young reasercher,
Laboratory of biophysics,
Institute Joef tefan,
Ljubljana, Slovenia

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