Re: dihedral colvar

From: Giacomo Fiorin (
Date: Tue Jan 17 2017 - 20:47:39 CST

What you describe can't be a torsional angle, unless you define an
additional axis to represent the line where the two hypersurfaces (planes)

You can, however, compute the angle of the quasi-rigid rotation (e.g.
orientationAngle for the small-molecule ligand) in a rotated frame that is
defined by the protein as fittingGroup. There is an example for the use of
fittingGroup here:

For proteins, this is also numerically more stable than computing the
inertia eigenvectors because the identity of the atoms is tracked by doing
the same optimal alignment done in computing minimal RMSD.

For more details, please read the doc:

On Tue, Jan 17, 2017 at 8:11 PM, Stefano Guglielmo <> wrote:

> Dear NAMD users, is it possible to define a collective variable as a
> torsional angle between the principal axes of two molecules in a
> protein-ligand system?
> Thanks in advance
> Stefano.
> --
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
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Phone: +1-215-204-4213
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the computers instead of the computers running us."*  - Steve Oualline

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