From: Axel Kohlmeyer (
Date: Fri Nov 19 2010 - 13:35:45 CST

On Fri, 2010-11-19 at 19:44 +0100, Branko wrote:
> Axel,
> I use gyration as colvar (in combination with distance) to obtain 3D
> free energy surface for set of molecules. Gyration – colvar as
> defined in NAMD manual do not include masses of atoms included.
> When I analyze trajectory and measure rgyr of atoms defined by colvar
> used, accordance is OK, as far as heavy atoms Br and Cl are not part
> of molecule. Please let me know next:
> 1. Is colvar used in ABF include atomic masses (if atoms are
> described as “atomNumbers”), or simply measure radius of gyration of
> atomic positions (providing that every position have a same weight).

you have to ask this the authors of the colvars package.

> 1. How (explicitly) to include mass as weighting factor in script
> that you made previously.

you can (and should) look this up in the VMD user's guide.

> 1. Is “measure rgyr selection” (providing that selection is
> “index”) give output comparable with colvar that I use in ABF
> calculation (see under 1).

again, this is a question to the colvars authors.
the only VMD related aspect here are periodic boundaries.
measure rgyr does not take them into account. you have
to use pbctools to transform/unwrap your trajectory
accordingly, if needed.


> Thanks
> Branko

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.