Re: Dihedral definition in NAMD

From: Giacomo Fiorin (
Date: Tue Mar 10 2015 - 06:28:26 CDT

The center of mass is not mentioned explicitly for all components, but
these are all consistent with the distance:
i.e. the groups' centers-of-mass are used to define individual points.

The only occasion where centers of geometry are used is for rotational fits.

Regarding the dihedral definition, how about taking a look at Figure 2 in
the same Wikipedia article?

On Tue, Mar 10, 2015 at 12:19 PM, Kevin C Chan <>

> Dear Users,
> I am now trying to harmonically restraint a dihedral angle of four
> selections of atoms using colvar for a regular NPT simulation. However the
> colvar manual does not give clearly how it defined the dihedral angle from
> the 4 groups.
> For example, referring to figure 3 at wiki (
>, does a sequence - group 1 2
> 3 4 means that group 2 and 3 are overlapped and angle between b1(1-2) and
> b2(4-3) is measured?
> Also, how actually does the colvar treat a selection of atom when
> calculating the distances or angles? Is it using the center of mass or
> center of geometry?
> Thanks in advance,
> Kevin
> City University of Hong Kong

Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213

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